phosphoglycerate dehydrogenase [Aeromonas bivalvium]
Protein Classification
phosphoglycerate dehydrogenase( domain architecture ID 11485509)
phosphoglycerate dehydrogenase catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, the first step in serine biosynthesis
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||||
| PRK11790 | PRK11790 | phosphoglycerate dehydrogenase; |
2-410 | 0e+00 | |||||||
phosphoglycerate dehydrogenase; : Pssm-ID: 236985 [Multi-domain] Cd Length: 409 Bit Score: 855.63 E-value: 0e+00
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| Name | Accession | Description | Interval | E-value | |||||||
| PRK11790 | PRK11790 | phosphoglycerate dehydrogenase; |
2-410 | 0e+00 | |||||||
phosphoglycerate dehydrogenase; Pssm-ID: 236985 [Multi-domain] Cd Length: 409 Bit Score: 855.63 E-value: 0e+00
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| PGDH_3 | cd12176 | Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate ... |
12-316 | 0e+00 | |||||||
Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Pssm-ID: 240653 Cd Length: 304 Bit Score: 572.60 E-value: 0e+00
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| SerA | COG0111 | Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism]; ... |
13-327 | 2.30e-132 | |||||||
Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism]; Phosphoglycerate dehydrogenase or related dehydrogenase is part of the Pathway/BioSystem: Serine biosynthesis Pssm-ID: 439881 [Multi-domain] Cd Length: 314 Bit Score: 382.62 E-value: 2.30e-132
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| 2-Hacid_dh | pfam00389 | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; This family represents the ... |
14-327 | 2.62e-96 | |||||||
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain. Pssm-ID: 425656 [Multi-domain] Cd Length: 311 Bit Score: 290.73 E-value: 2.62e-96
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| PGDH | TIGR01327 | D-3-phosphoglycerate dehydrogenase; This model represents a long form of D-3-phosphoglycerate ... |
13-329 | 1.21e-88 | |||||||
D-3-phosphoglycerate dehydrogenase; This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli. [Amino acid biosynthesis, Serine family] Pssm-ID: 273556 [Multi-domain] Cd Length: 525 Bit Score: 278.05 E-value: 1.21e-88
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| Name | Accession | Description | Interval | E-value | |||||||
| PRK11790 | PRK11790 | phosphoglycerate dehydrogenase; |
2-410 | 0e+00 | |||||||
phosphoglycerate dehydrogenase; Pssm-ID: 236985 [Multi-domain] Cd Length: 409 Bit Score: 855.63 E-value: 0e+00
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| PGDH_3 | cd12176 | Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate ... |
12-316 | 0e+00 | |||||||
Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Pssm-ID: 240653 Cd Length: 304 Bit Score: 572.60 E-value: 0e+00
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| SerA | COG0111 | Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism]; ... |
13-327 | 2.30e-132 | |||||||
Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism]; Phosphoglycerate dehydrogenase or related dehydrogenase is part of the Pathway/BioSystem: Serine biosynthesis Pssm-ID: 439881 [Multi-domain] Cd Length: 314 Bit Score: 382.62 E-value: 2.30e-132
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| PGDH_4 | cd12173 | Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate ... |
13-316 | 5.75e-113 | |||||||
Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Pssm-ID: 240650 [Multi-domain] Cd Length: 304 Bit Score: 332.84 E-value: 5.75e-113
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| formate_dh_like | cd05198 | Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase ... |
13-316 | 1.83e-103 | |||||||
Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family; Formate dehydrogenase, D-specific 2-hydroxy acid dehydrogenase, Phosphoglycerate Dehydrogenase, Lactate dehydrogenase, Thermostable Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate reductase, among others, share a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production and in the stress responses of plants. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase, among others. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240622 [Multi-domain] Cd Length: 302 Bit Score: 308.40 E-value: 1.83e-103
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| PGDH_2 | cd05303 | Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Phosphoglycerate ... |
12-316 | 1.34e-101 | |||||||
Phosphoglycerate dehydrogenase (PGDH) NAD-binding and catalytic domains; Phosphoglycerate dehydrogenase (PGDH) catalyzes the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDH comes in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Pssm-ID: 240628 [Multi-domain] Cd Length: 301 Bit Score: 303.69 E-value: 1.34e-101
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| 2-Hacid_dh | pfam00389 | D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; This family represents the ... |
14-327 | 2.62e-96 | |||||||
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain; This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain. Pssm-ID: 425656 [Multi-domain] Cd Length: 311 Bit Score: 290.73 E-value: 2.62e-96
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| LdhA | COG1052 | Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase [Energy production and conversion, ... |
11-327 | 1.68e-93 | |||||||
Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase [Energy production and conversion, Coenzyme transport and metabolism, General function prediction only]; Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis Pssm-ID: 440672 [Multi-domain] Cd Length: 316 Bit Score: 283.52 E-value: 1.68e-93
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| PGDH_like_2 | cd12172 | Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; ... |
13-316 | 2.81e-92 | |||||||
Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. Pssm-ID: 240649 [Multi-domain] Cd Length: 306 Bit Score: 280.14 E-value: 2.81e-92
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| PGDH | TIGR01327 | D-3-phosphoglycerate dehydrogenase; This model represents a long form of D-3-phosphoglycerate ... |
13-329 | 1.21e-88 | |||||||
D-3-phosphoglycerate dehydrogenase; This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli. [Amino acid biosynthesis, Serine family] Pssm-ID: 273556 [Multi-domain] Cd Length: 525 Bit Score: 278.05 E-value: 1.21e-88
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| 2-Hacid_dh_13 | cd12178 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
40-327 | 1.15e-79 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240655 [Multi-domain] Cd Length: 317 Bit Score: 248.30 E-value: 1.15e-79
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| 2-Hacid_dh_11 | cd12175 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
13-310 | 3.59e-79 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240652 [Multi-domain] Cd Length: 311 Bit Score: 246.72 E-value: 3.59e-79
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| 2-Hacid_dh_4 | cd12162 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
44-305 | 6.12e-77 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240639 [Multi-domain] Cd Length: 307 Bit Score: 240.82 E-value: 6.12e-77
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| PGDH_like_3 | cd12174 | Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; ... |
70-327 | 6.16e-76 | |||||||
Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. Pssm-ID: 240651 [Multi-domain] Cd Length: 305 Bit Score: 238.23 E-value: 6.16e-76
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| 2-Hacid_dh_10 | cd12171 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
45-304 | 7.26e-73 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240648 [Multi-domain] Cd Length: 310 Bit Score: 230.50 E-value: 7.26e-73
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| CtBP_dh | cd05299 | C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related ... |
13-314 | 1.02e-71 | |||||||
C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related repressor; The transcriptional corepressor CtBP is a dehydrogenase with sequence and structural similarity to the d2-hydroxyacid dehydrogenase family. CtBP was initially identified as a protein that bound the PXDLS sequence at the adenovirus E1A C terminus, causing the loss of CR-1-mediated transactivation. CtBP binds NAD(H) within a deep cleft, undergoes a conformational change upon NAD binding, and has NAD-dependent dehydrogenase activity. Pssm-ID: 240624 [Multi-domain] Cd Length: 312 Bit Score: 227.40 E-value: 1.02e-71
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| GDH | cd05301 | D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); D-glycerate dehydrogenase (GDH, ... |
40-314 | 1.18e-64 | |||||||
D-glycerate dehydrogenase/hydroxypyruvate reductase (GDH); D-glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase, HPR) catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. In humans, HPR deficiency causes primary hyperoxaluria type 2, characterized by over-excretion of L-glycerate and oxalate in the urine, possibly due to an imbalance in competition with L-lactate dehydrogenase, another formate dehydrogenase (FDH)-like enzyme. GDH, like FDH and other members of the D-specific hydroxyacid dehydrogenase family that also includes L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase, typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form, despite often low sequence identity. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240626 [Multi-domain] Cd Length: 309 Bit Score: 209.17 E-value: 1.18e-64
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| GDH_like_1 | cd12161 | Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy ... |
13-303 | 4.51e-63 | |||||||
Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, aka Hydroxypyruvate Reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240638 [Multi-domain] Cd Length: 315 Bit Score: 205.15 E-value: 4.51e-63
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| 2-Hacid_dh_C | pfam02826 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; This domain is inserted ... |
118-295 | 2.41e-60 | |||||||
D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389. Pssm-ID: 427007 [Multi-domain] Cd Length: 178 Bit Score: 193.48 E-value: 2.41e-60
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| 2-Hacid_dh_14 | cd12179 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
13-313 | 4.18e-60 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240656 [Multi-domain] Cd Length: 306 Bit Score: 197.52 E-value: 4.18e-60
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| Mand_dh_like | cd12168 | D-Mandelate Dehydrogenase-like dehydrogenases; D-Mandelate dehydrogenase (D-ManDH), identified ... |
86-309 | 5.19e-60 | |||||||
D-Mandelate Dehydrogenase-like dehydrogenases; D-Mandelate dehydrogenase (D-ManDH), identified as an enzyme that interconverts benzoylformate and D-mandelate, is a D-2-hydroxyacid dehydrogenase family member that catalyzes the conversion of c3-branched 2-ketoacids. D-ManDH exhibits broad substrate specificities for 2-ketoacids with large hydrophobic side chains, particularly those with C3-branched side chains. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Glycerate dehydrogenase catalyzes the reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240645 [Multi-domain] Cd Length: 321 Bit Score: 197.38 E-value: 5.19e-60
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| PGDH_like_1 | cd12169 | Putative D-3-Phosphoglycerate Dehydrogenases; Phosphoglycerate dehydrogenases (PGDHs) catalyze ... |
41-304 | 4.63e-58 | |||||||
Putative D-3-Phosphoglycerate Dehydrogenases; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. Pssm-ID: 240646 [Multi-domain] Cd Length: 308 Bit Score: 191.96 E-value: 4.63e-58
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| 2-Hacid_dh_8 | cd12167 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
41-309 | 6.98e-57 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240644 [Multi-domain] Cd Length: 330 Bit Score: 189.69 E-value: 6.98e-57
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| PRK06487 | PRK06487 | 2-hydroxyacid dehydrogenase; |
39-327 | 2.44e-56 | |||||||
2-hydroxyacid dehydrogenase; Pssm-ID: 180588 [Multi-domain] Cd Length: 317 Bit Score: 187.98 E-value: 2.44e-56
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| LDH_like | cd01619 | D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; D-Lactate ... |
21-305 | 5.44e-55 | |||||||
D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the Rossmann fold typical of many NAD binding proteins. D-HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. Similar to the structurally distinct L-HicDH, D-HicDH exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240620 [Multi-domain] Cd Length: 323 Bit Score: 184.43 E-value: 5.44e-55
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| 2-Hacid_dh_12 | cd12177 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
22-327 | 8.56e-55 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240654 [Multi-domain] Cd Length: 321 Bit Score: 184.06 E-value: 8.56e-55
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| HPPR | cd12156 | Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; ... |
12-301 | 9.04e-54 | |||||||
Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the NADP-dependent reduction of hydroxyphenylpyruvates, hydroxypyruvate, or pyruvate to its respective lactate. HPPR acts as a dimer and is related to D-isomer-specific 2-hydroxyacid dehydrogenases, a superfamily that includes groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240633 [Multi-domain] Cd Length: 301 Bit Score: 180.74 E-value: 9.04e-54
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| PRK13243 | PRK13243 | glyoxylate reductase; Reviewed |
11-316 | 9.86e-54 | |||||||
glyoxylate reductase; Reviewed Pssm-ID: 183914 Cd Length: 333 Bit Score: 181.53 E-value: 9.86e-54
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| LDH | cd12186 | D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding ... |
18-305 | 3.99e-53 | |||||||
D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding and catalytic domains; D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenases family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240662 Cd Length: 329 Bit Score: 179.65 E-value: 3.99e-53
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| LDH_like_1 | cd12187 | D-Lactate and related Dehydrogenase like proteins, NAD-binding and catalytic domains; ... |
63-305 | 1.46e-51 | |||||||
D-Lactate and related Dehydrogenase like proteins, NAD-binding and catalytic domains; D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-Hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-2-hydroxyisocaproate dehydrogenase-like (HicDH) proteins are NAD-dependent members of the hydroxycarboxylate dehydrogenase family, and share the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240663 [Multi-domain] Cd Length: 329 Bit Score: 175.93 E-value: 1.46e-51
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| ErythrP_dh | cd12158 | D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; ... |
42-301 | 6.27e-50 | |||||||
D-Erythronate-4-Phosphate Dehydrogenase NAD-binding and catalytic domains; D-Erythronate-4-phosphate Dehydrogenase (E. coli gene PdxB), a D-specific 2-hydroxyacid dehydrogenase family member, catalyzes the NAD-dependent oxidation of erythronate-4-phosphate, which is followed by transamination to form 4-hydroxy-L-threonine-4-phosphate within the de novo biosynthesis pathway of vitamin B6. D-Erythronate-4-phosphate dehydrogenase has the common architecture shared with D-isomer specific 2-hydroxyacid dehydrogenases but contains an additional C-terminal dimerization domain in addition to an NAD-binding domain and the "lid" domain. The lid domain corresponds to the catalytic domain of phosphoglycerate dehydrogenase and other proteins of the D-isomer specific 2-hydroxyacid dehydrogenase family, which include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Pssm-ID: 240635 [Multi-domain] Cd Length: 343 Bit Score: 171.94 E-value: 6.27e-50
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| PRK06932 | PRK06932 | 2-hydroxyacid dehydrogenase; |
36-320 | 1.32e-48 | |||||||
2-hydroxyacid dehydrogenase; Pssm-ID: 235890 [Multi-domain] Cd Length: 314 Bit Score: 167.67 E-value: 1.32e-48
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| 2-Hacid_dh_6 | cd12165 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
38-320 | 8.84e-48 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240642 [Multi-domain] Cd Length: 314 Bit Score: 165.49 E-value: 8.84e-48
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| PTDH | cd12157 | Thermostable Phosphite Dehydrogenase; Phosphite dehydrogenase (PTDH), a member of the ... |
13-315 | 1.73e-47 | |||||||
Thermostable Phosphite Dehydrogenase; Phosphite dehydrogenase (PTDH), a member of the D-specific 2-hydroxyacid dehydrogenase family, catalyzes the NAD-dependent formation of phosphate from phosphite (hydrogen phosphonate). PTDH has been suggested as a potential enzyme for cofactor regeneration systems. The D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD-binding domain. Pssm-ID: 240634 [Multi-domain] Cd Length: 318 Bit Score: 164.77 E-value: 1.73e-47
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| PRK08410 | PRK08410 | D-2-hydroxyacid dehydrogenase; |
26-305 | 3.76e-47 | |||||||
D-2-hydroxyacid dehydrogenase; Pssm-ID: 181414 [Multi-domain] Cd Length: 311 Bit Score: 163.62 E-value: 3.76e-47
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| LDH_like_2 | cd12183 | D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; D-Lactate ... |
84-305 | 3.31e-45 | |||||||
D-Lactate and related Dehydrogenases, NAD-binding and catalytic domains; D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenase family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase (D-HicDH) and shares the 2-domain structure of formate dehydrogenase. D-2-hydroxyisocaproate dehydrogenase-like (HicDH) proteins are NAD-dependent members of the hydroxycarboxylate dehydrogenase family, and share the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240659 Cd Length: 328 Bit Score: 159.15 E-value: 3.31e-45
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| 2-Hacid_dh_1 | cd05300 | Putative D-isomer specific 2-hydroxyacid dehydrogenase; 2-Hydroxyacid dehydrogenases catalyze ... |
13-305 | 2.39e-43 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenase; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomains but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of the hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production and in the stress responses of plants. Pssm-ID: 240625 [Multi-domain] Cd Length: 313 Bit Score: 153.45 E-value: 2.39e-43
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| FDH | cd05302 | NAD-dependent Formate Dehydrogenase (FDH); NAD-dependent formate dehydrogenase (FDH) catalyzes ... |
66-303 | 8.82e-43 | |||||||
NAD-dependent Formate Dehydrogenase (FDH); NAD-dependent formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of a formate anion to carbon dioxide coupled with the reduction of NAD+ to NADH. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family have 2 highly similar subdomains of the alpha/beta form, with NAD binding occurring in the cleft between subdomains. NAD contacts are primarily to the Rossmann-fold NAD-binding domain which is inserted within the linear sequence of the more diverse flavodoxin-like catalytic subdomain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of the hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production from C1 compounds such as methanol, and in the stress responses of plants. NAD-dependent FDH is useful in cofactor regeneration in asymmetrical biocatalytic reduction processes, where FDH irreversibly oxidizes formate to carbon dioxide, while reducing the oxidized form of the cofactor to the reduced form. Pssm-ID: 240627 Cd Length: 348 Bit Score: 153.25 E-value: 8.82e-43
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| PRK07574 | PRK07574 | NAD-dependent formate dehydrogenase; |
85-302 | 7.32e-40 | |||||||
NAD-dependent formate dehydrogenase; Pssm-ID: 181041 Cd Length: 385 Bit Score: 146.36 E-value: 7.32e-40
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| HGDH_LDH_like | cd12185 | Putative Lactate dehydrogenase and (R)-2-Hydroxyglutarate Dehydrogenase-like proteins, ... |
26-305 | 4.71e-39 | |||||||
Putative Lactate dehydrogenase and (R)-2-Hydroxyglutarate Dehydrogenase-like proteins, NAD-binding and catalytic domains; This group contains various putative dehydrogenases related to D-lactate dehydrogenase (LDH), (R)-2-hydroxyglutarate dehydrogenase (HGDH), and related enzymes, members of the 2-hydroxyacid dehydrogenases family. LDH catalyzes the interconversion of pyruvate and lactate, and HGDH catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. Despite often low sequence identity within this 2-hydroxyacid dehydrogenase family, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240661 Cd Length: 322 Bit Score: 142.35 E-value: 4.71e-39
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| HGDH_like | cd12184 | (R)-2-Hydroxyglutarate Dehydrogenase and related dehydrogenases, NAD-binding and catalytic ... |
85-304 | 3.33e-38 | |||||||
(R)-2-Hydroxyglutarate Dehydrogenase and related dehydrogenases, NAD-binding and catalytic domains; (R)-2-hydroxyglutarate dehydrogenase (HGDH) catalyzes the NAD-dependent reduction of 2-oxoglutarate to (R)-2-hydroxyglutarate. HGDH is a member of the D-2-hydroxyacid NAD(+)-dependent dehydrogenase family; these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240660 Cd Length: 330 Bit Score: 140.51 E-value: 3.33e-38
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| PRK00257 | PRK00257 | 4-phosphoerythronate dehydrogenase PdxB; |
52-296 | 2.57e-35 | |||||||
4-phosphoerythronate dehydrogenase PdxB; Pssm-ID: 166874 [Multi-domain] Cd Length: 381 Bit Score: 134.01 E-value: 2.57e-35
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| PGDH_1 | cd12155 | Phosphoglycerate Dehydrogenase, 2-hydroxyacid dehydrogenase family; Phosphoglycerate ... |
85-303 | 1.00e-33 | |||||||
Phosphoglycerate Dehydrogenase, 2-hydroxyacid dehydrogenase family; Phosphoglycerate Dehydrogenase (PGDH) catalyzes the NAD-dependent conversion of 3-phosphoglycerate into 3-phosphohydroxypyruvate, which is the first step in serine biosynthesis. Over-expression of PGDH has been implicated as supporting proliferation of certain breast cancers, while PGDH deficiency is linked to defects in mammalian central nervous system development. PGDH is a member of the 2-hydroxyacid dehydrogenase family, enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240632 [Multi-domain] Cd Length: 314 Bit Score: 128.08 E-value: 1.00e-33
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| 2-Hacid_dh_7 | cd12166 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
45-298 | 1.31e-33 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240643 [Multi-domain] Cd Length: 300 Bit Score: 127.32 E-value: 1.31e-33
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| PLN03139 | PLN03139 | formate dehydrogenase; Provisional |
85-302 | 1.21e-30 | |||||||
formate dehydrogenase; Provisional Pssm-ID: 178684 Cd Length: 386 Bit Score: 121.11 E-value: 1.21e-30
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| PRK15409 | PRK15409 | glyoxylate/hydroxypyruvate reductase GhrB; |
71-305 | 2.78e-30 | |||||||
glyoxylate/hydroxypyruvate reductase GhrB; Pssm-ID: 185307 Cd Length: 323 Bit Score: 118.70 E-value: 2.78e-30
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| ACT_3PGDH | cd04901 | C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in ... |
341-409 | 1.75e-29 | |||||||
C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria; The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. Members of this CD belong to the superfamily of ACT regulatory domains. Pssm-ID: 153173 Cd Length: 69 Bit Score: 109.13 E-value: 1.75e-29
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| 2-Hacid_dh_5 | cd12163 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
104-309 | 3.47e-29 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240640 Cd Length: 334 Bit Score: 116.22 E-value: 3.47e-29
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| PRK12480 | PRK12480 | D-lactate dehydrogenase; Provisional |
86-310 | 1.59e-27 | |||||||
D-lactate dehydrogenase; Provisional Pssm-ID: 183550 Cd Length: 330 Bit Score: 111.54 E-value: 1.59e-27
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| PLN02928 | PLN02928 | oxidoreductase family protein |
46-310 | 5.97e-27 | |||||||
oxidoreductase family protein Pssm-ID: 215501 Cd Length: 347 Bit Score: 110.16 E-value: 5.97e-27
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| PRK08605 | PRK08605 | D-lactate dehydrogenase; Validated |
86-327 | 1.07e-26 | |||||||
D-lactate dehydrogenase; Validated Pssm-ID: 181499 Cd Length: 332 Bit Score: 109.06 E-value: 1.07e-26
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| GDH_like_2 | cd12164 | Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy ... |
110-299 | 2.94e-26 | |||||||
Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240641 [Multi-domain] Cd Length: 306 Bit Score: 107.20 E-value: 2.94e-26
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| 2-Hacid_dh_15 | cd12180 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
97-326 | 3.07e-26 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240657 Cd Length: 308 Bit Score: 107.43 E-value: 3.07e-26
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| 2-Hacid_dh_2 | cd12159 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
112-311 | 6.78e-26 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240636 Cd Length: 303 Bit Score: 106.20 E-value: 6.78e-26
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| 2-Hacid_dh_9 | cd12170 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
44-316 | 4.24e-25 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240647 [Multi-domain] Cd Length: 294 Bit Score: 103.92 E-value: 4.24e-25
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| PLN02306 | PLN02306 | hydroxypyruvate reductase |
40-316 | 1.85e-24 | |||||||
hydroxypyruvate reductase Pssm-ID: 177941 Cd Length: 386 Bit Score: 103.78 E-value: 1.85e-24
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| ACT_3PGDH-like | cd04879 | ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate ... |
341-409 | 2.17e-20 | |||||||
ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. This CD also includes the C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillus, and Treponema species. LSD enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in E. coli, and other Enterobacteriales, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains. Pssm-ID: 153151 Cd Length: 71 Bit Score: 84.44 E-value: 2.17e-20
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| 2-Hacid_dh_3 | cd12160 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
111-305 | 5.83e-20 | |||||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240637 Cd Length: 310 Bit Score: 89.74 E-value: 5.83e-20
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| PRK15438 | PRK15438 | erythronate-4-phosphate dehydrogenase PdxB; Provisional |
49-302 | 3.32e-19 | |||||||
erythronate-4-phosphate dehydrogenase PdxB; Provisional Pssm-ID: 185335 [Multi-domain] Cd Length: 378 Bit Score: 88.43 E-value: 3.32e-19
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| PRK06436 | PRK06436 | 2-hydroxyacid dehydrogenase; |
112-320 | 1.10e-18 | |||||||
2-hydroxyacid dehydrogenase; Pssm-ID: 235800 [Multi-domain] Cd Length: 303 Bit Score: 85.70 E-value: 1.10e-18
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| FDH_GDH_like | cd12154 | Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related ... |
31-271 | 1.50e-16 | |||||||
Formate/glycerate dehydrogenases, D-specific 2-hydroxy acid dehydrogenases and related dehydrogenases; The formate/glycerate dehydrogenase like family contains a diverse group of enzymes such as formate dehydrogenase (FDH), glycerate dehydrogenase (GDH), D-lactate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine hydrolase, that share a common 2-domain structure. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar domains of the alpha/beta Rossmann fold NAD+ binding form. The NAD(P) binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD(P) is bound, primarily to the C-terminal portion of the 2nd (internal) domain. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of a hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. Pssm-ID: 240631 [Multi-domain] Cd Length: 310 Bit Score: 79.97 E-value: 1.50e-16
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| ghrA | PRK15469 | glyoxylate/hydroxypyruvate reductase GhrA; |
198-302 | 8.85e-09 | |||||||
glyoxylate/hydroxypyruvate reductase GhrA; Pssm-ID: 185366 Cd Length: 312 Bit Score: 56.34 E-value: 8.85e-09
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| ACT | cd02116 | ACT domains are commonly involved in specifically binding an amino acid or other small ligand ... |
342-398 | 2.30e-05 | |||||||
ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme; Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-prephenate dehydratase enzyme (P-protein), respectively. Aspartokinases typically consist of two C-terminal ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. ACT domain repeats have been shown to have nonequivalent ligand-binding sites with complex regulatory patterns such as those seen in the bifunctional enzyme, aspartokinase-homoserine dehydrogenase (ThrA). In other enzymes, such as phenylalanine hydroxylases, the ACT domain appears to function as a flexible small module providing allosteric regulation via transmission of conformational changes, these conformational changes are not necessarily initiated by regulatory ligand binding at the ACT domain itself. ACT domains are present either singularly, N- or C-terminal, or in pairs present C-terminal or between two catalytic domains. Unique to cyanobacteria are four ACT domains C-terminal to an aspartokinase domain. A few proteins are composed almost entirely of ACT domain repeats as seen in the four ACT domain protein, the ACR protein, found in higher plants; and the two ACT domain protein, the glycine cleavage system transcriptional repressor (GcvR) protein, found in some bacteria. Also seen are single ACT domain proteins similar to the Streptococcus pneumoniae ACT domain protein (uncharacterized pdb structure 1ZPV) found in both bacteria and archaea. Purportedly, the ACT domain is an evolutionarily mobile ligand binding regulatory module that has been fused to different enzymes at various times. Pssm-ID: 153139 [Multi-domain] Cd Length: 60 Bit Score: 41.89 E-value: 2.30e-05
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| ACT_3PGDH-xct | cd04902 | C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); The ... |
346-409 | 1.30e-04 | |||||||
C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH); The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between identical domains in the asymmetric unit. How this asymmetry influences the mechanism of effector inhibition is still unknown. Members of this CD belong to the superfamily of ACT regulatory domains. Pssm-ID: 153174 Cd Length: 73 Bit Score: 40.15 E-value: 1.30e-04
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| ACT | pfam01842 | ACT domain; This family of domains generally have a regulatory role. ACT domains are linked to ... |
347-402 | 5.66e-04 | |||||||
ACT domain; This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95, which is inhibited by serine. Aspartokinase EC:2.7.2.4, which is regulated by lysine. Acetolactate synthase small regulatory subunit, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51. formyltetrahydrofolate deformylase EC:3.5.1.10, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 Pssm-ID: 426468 [Multi-domain] Cd Length: 66 Bit Score: 38.06 E-value: 5.66e-04
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| SpoT | COG0317 | (p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]; |
343-407 | 7.51e-04 | |||||||
(p)ppGpp synthase/hydrolase, HD superfamily [Signal transduction mechanisms, Transcription]; Pssm-ID: 440086 [Multi-domain] Cd Length: 722 Bit Score: 41.68 E-value: 7.51e-04
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| ACT_LSD | cd04903 | C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; ... |
342-409 | 2.72e-03 | |||||||
C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit; The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains. Pssm-ID: 153175 Cd Length: 71 Bit Score: 36.36 E-value: 2.72e-03
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| ACT_RelA-SpoT | cd04876 | ACT domain found C-terminal of the RelA/SpoT domains; ACT_RelA-SpoT: the ACT domain found ... |
347-407 | 3.37e-03 | |||||||
ACT domain found C-terminal of the RelA/SpoT domains; ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes in E. coli, a bifunctional Rel/Spo protein has been discovered in most gram-positive organisms studied so far. These bifunctional Rel/Spo homologs (rsh) appear to modulate (p)ppGpp levels through two distinct active sites that are controlled by a reciprocal regulatory mechanism ensuring inverse coupling of opposing activities. In studies with the Streptococcus equisimilis Rel/Spo homolog, the C-terminal domain appears to be involved in this reciprocal regulation of the two opposing catalytic activities present in the N-terminal domain, ensuring that both synthesis and degradation activities are not coinduced. Members of this CD belong to the superfamily of ACT regulatory domains. Pssm-ID: 153148 [Multi-domain] Cd Length: 71 Bit Score: 35.89 E-value: 3.37e-03
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| ACT_4 | pfam13291 | ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains. These ACT ... |
347-407 | 6.58e-03 | |||||||
ACT domain; ACT domains bind to amino acids and regulate associated enzyme domains. These ACT domains are found at the C-terminus of the RelA protein. Pssm-ID: 463831 [Multi-domain] Cd Length: 79 Bit Score: 35.23 E-value: 6.58e-03
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