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Conserved domains on  [gi|2179479887|ref|WP_234835366|]
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NADPH-dependent F420 reductase [Sinorhizobium meliloti]

Protein Classification

NADPH-dependent F420 reductase( domain architecture ID 11449986)

NADPH-dependent F420 reductase may be part of a F420-dependent NADP oxidoreductase catalyzing the reduction of NADP(+) with F420H(2) via hydride transfer, as well as the reverse reaction, the reduction of F420 with NADPH

CATH:  3.40.50.720
EC:  1.-.-.-
Gene Ontology:  GO:0052851|GO:0016491|GO:0070967|GO:0016651
SCOP:  4000104

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG2085 COG2085
Predicted dinucleotide-binding enzyme [General function prediction only];
4-136 1.42e-38

Predicted dinucleotide-binding enzyme [General function prediction only];


:

Pssm-ID: 441688 [Multi-domain]  Cd Length: 205  Bit Score: 130.29  E-value: 1.42e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   4 YAIIGAGAIGSALAERFTAAQIPAIIAnSRGPASLSSVTDRFGASVKAVELKDAL-QADVVILAVPYDSIADIVTQVSD- 81
Cdd:COG2085     1 IGIIGTGNIGSALARRLAAAGHEVVIG-SRDPEKAAALAAELGPGARAGTNAEAAaAADVVVLAVPYEAVPDVLESLGDa 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2179479887  82 WGGRIVVDASNAIDFPAFKPRDLGGRLST-EIVSELVPGAKVVKAFNTLPAAVLAE 136
Cdd:COG2085    80 LAGKIVIDATNPLPERDGFILDPPGGGSAaELVAALLPGARVVKAFNTIGAAVLAD 135
 
Name Accession Description Interval E-value
COG2085 COG2085
Predicted dinucleotide-binding enzyme [General function prediction only];
4-136 1.42e-38

Predicted dinucleotide-binding enzyme [General function prediction only];


Pssm-ID: 441688 [Multi-domain]  Cd Length: 205  Bit Score: 130.29  E-value: 1.42e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   4 YAIIGAGAIGSALAERFTAAQIPAIIAnSRGPASLSSVTDRFGASVKAVELKDAL-QADVVILAVPYDSIADIVTQVSD- 81
Cdd:COG2085     1 IGIIGTGNIGSALARRLAAAGHEVVIG-SRDPEKAAALAAELGPGARAGTNAEAAaAADVVVLAVPYEAVPDVLESLGDa 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2179479887  82 WGGRIVVDASNAIDFPAFKPRDLGGRLST-EIVSELVPGAKVVKAFNTLPAAVLAE 136
Cdd:COG2085    80 LAGKIVIDATNPLPERDGFILDPPGGGSAaELVAALLPGARVVKAFNTIGAAVLAD 135
F420_oxidored pfam03807
NADP oxidoreductase coenzyme F420-dependent;
5-92 1.38e-15

NADP oxidoreductase coenzyme F420-dependent;


Pssm-ID: 397743 [Multi-domain]  Cd Length: 92  Bit Score: 67.64  E-value: 1.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   5 AIIGAGAIGSALAERFTAA-QIPAIIANSRGPASLSSVTDRFGASVKAVELKDALQ-ADVVILAVPYDSIADIVTQVSD- 81
Cdd:pfam03807   1 GFIGAGNMGEALARGLVAAgPHEVVVANSRNPEKAEELAEEYGVGATAVDNEEAAEeADVVFLAVKPEDAPDVLSELSDl 80

                          90
                  ....*....|.
gi 2179479887  82 WGGRIVVDASN 92
Cdd:pfam03807  81 LKGKIVISIAA 91
npdG TIGR01915
NADPH-dependent F420 reductase; This model represents a subset of a parent family described by ...
 8-137 1.07e-09

NADPH-dependent F420 reductase; This model represents a subset of a parent family described by pfam03807. Unlike the parent family, members of this family are found only in species with evidence of coenzyme F420. All members of this family are believed to act as NADPH-dependent F420 reductase. [Energy metabolism, Electron transport]


Pssm-ID: 273873  Cd Length: 219  Bit Score: 54.80  E-value: 1.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   8 GAGAIGSALAERFtAAQIPAIIANSRGP--------ASLSSVTDR-FGASVKAVELKDAL-QADVVILAVPYDSIADIVT 77
Cdd:TIGR01915   8 GTGDQGKGLALRL-AKAGNKIIIGSRDLekaeeaaaKALEELGHGgSDIKVTGADNAEAAkRADVVILAVPWDHVLKTLE 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2179479887  78 QVSD-WGGRIVVDASNAIDFPAFKP---RDLGGRLSTEIVSELVP-GAKVVKAFNTLPAAVLAEI 137
Cdd:TIGR01915  87 SLRDeLSGKLVISPVVPLASDGGKGaryLPPEEGSAAEQAAALLPeTSRVVAAFHNLSAVLLQDV 151
PRK11880 PRK11880
pyrroline-5-carboxylate reductase; Reviewed
 1-88 4.08e-09

pyrroline-5-carboxylate reductase; Reviewed


Pssm-ID: 237008 [Multi-domain]  Cd Length: 267  Bit Score: 53.61  E-value: 4.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   1 MTTYAIIGAGAIGSALAERFTAAQIPA--IIANSRGPASLSSVTDRFGASVKAVELKDALQADVVILAV-PYDsIADIVT 77
Cdd:PRK11880    2 MKKIGFIGGGNMASAIIGGLLASGVPAkdIIVSDPSPEKRAALAEEYGVRAATDNQEAAQEADVVVLAVkPQV-MEEVLS 80

                          90
                  ....*....|.
gi 2179479887  78 QVSDWGGRIVV 88
Cdd:PRK11880   81 ELKGQLDKLVV 91
2-Hacid_dh_11 cd12175
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ...
 3-69 1.50e-04

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: 40.63  E-value: 1.50e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2179479887   3 TYAIIGAGAIGSALAERFTAAQiPAIIANSRGPASlSSVTDRFGASvkAVELKDALQ-ADVVILAVPY 69
Cdd:cd12175   144 TVGIVGLGNIGRAVARRLRGFG-VEVIYYDRFRDP-EAEEKDLGVR--YVELDELLAeSDVVSLHVPL 207
 
Name Accession Description Interval E-value
COG2085 COG2085
Predicted dinucleotide-binding enzyme [General function prediction only];
4-136 1.42e-38

Predicted dinucleotide-binding enzyme [General function prediction only];


Pssm-ID: 441688 [Multi-domain]  Cd Length: 205  Bit Score: 130.29  E-value: 1.42e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   4 YAIIGAGAIGSALAERFTAAQIPAIIAnSRGPASLSSVTDRFGASVKAVELKDAL-QADVVILAVPYDSIADIVTQVSD- 81
Cdd:COG2085     1 IGIIGTGNIGSALARRLAAAGHEVVIG-SRDPEKAAALAAELGPGARAGTNAEAAaAADVVVLAVPYEAVPDVLESLGDa 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2179479887  82 WGGRIVVDASNAIDFPAFKPRDLGGRLST-EIVSELVPGAKVVKAFNTLPAAVLAE 136
Cdd:COG2085    80 LAGKIVIDATNPLPERDGFILDPPGGGSAaELVAALLPGARVVKAFNTIGAAVLAD 135
F420_oxidored pfam03807
NADP oxidoreductase coenzyme F420-dependent;
5-92 1.38e-15

NADP oxidoreductase coenzyme F420-dependent;


Pssm-ID: 397743 [Multi-domain]  Cd Length: 92  Bit Score: 67.64  E-value: 1.38e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   5 AIIGAGAIGSALAERFTAA-QIPAIIANSRGPASLSSVTDRFGASVKAVELKDALQ-ADVVILAVPYDSIADIVTQVSD- 81
Cdd:pfam03807   1 GFIGAGNMGEALARGLVAAgPHEVVVANSRNPEKAEELAEEYGVGATAVDNEEAAEeADVVFLAVKPEDAPDVLSELSDl 80

                          90
                  ....*....|.
gi 2179479887  82 WGGRIVVDASN 92
Cdd:pfam03807  81 LKGKIVISIAA 91
COG5495 COG5495
Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains ...
 1-101 4.76e-10

Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains [General function prediction only];


Pssm-ID: 444246 [Multi-domain]  Cd Length: 286  Bit Score: 56.36  E-value: 4.76e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   1 MTTYAIIGAGAIGSALAERFTAAQIPAIIANSRGPASLSSVTDRFGASVKAVELKDALQADVVILAVPYDSIADIVTQVS 80
Cdd:COG5495     3 RMKIGIIGAGRVGTALAAALRAAGHEVVGVYSRSPASAERAAALLGAVPALDLEELAAEADLVLLAVPDDAIAEVAAGLA 82

                          90       100
                  ....*....|....*....|....*
gi 2179479887  81 DWG----GRIVVDASNAIDFPAFKP 101
Cdd:COG5495    83 AAGalrpGQLVVHTSGALGSDVLAP 107
npdG TIGR01915
NADPH-dependent F420 reductase; This model represents a subset of a parent family described by ...
 8-137 1.07e-09

NADPH-dependent F420 reductase; This model represents a subset of a parent family described by pfam03807. Unlike the parent family, members of this family are found only in species with evidence of coenzyme F420. All members of this family are believed to act as NADPH-dependent F420 reductase. [Energy metabolism, Electron transport]


Pssm-ID: 273873  Cd Length: 219  Bit Score: 54.80  E-value: 1.07e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   8 GAGAIGSALAERFtAAQIPAIIANSRGP--------ASLSSVTDR-FGASVKAVELKDAL-QADVVILAVPYDSIADIVT 77
Cdd:TIGR01915   8 GTGDQGKGLALRL-AKAGNKIIIGSRDLekaeeaaaKALEELGHGgSDIKVTGADNAEAAkRADVVILAVPWDHVLKTLE 86

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2179479887  78 QVSD-WGGRIVVDASNAIDFPAFKP---RDLGGRLSTEIVSELVP-GAKVVKAFNTLPAAVLAEI 137
Cdd:TIGR01915  87 SLRDeLSGKLVISPVVPLASDGGKGaryLPPEEGSAAEQAAALLPeTSRVVAAFHNLSAVLLQDV 151
PRK11880 PRK11880
pyrroline-5-carboxylate reductase; Reviewed
 1-88 4.08e-09

pyrroline-5-carboxylate reductase; Reviewed


Pssm-ID: 237008 [Multi-domain]  Cd Length: 267  Bit Score: 53.61  E-value: 4.08e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   1 MTTYAIIGAGAIGSALAERFTAAQIPA--IIANSRGPASLSSVTDRFGASVKAVELKDALQADVVILAV-PYDsIADIVT 77
Cdd:PRK11880    2 MKKIGFIGGGNMASAIIGGLLASGVPAkdIIVSDPSPEKRAALAEEYGVRAATDNQEAAQEADVVVLAVkPQV-MEEVLS 80

                          90
                  ....*....|.
gi 2179479887  78 QVSDWGGRIVV 88
Cdd:PRK11880   81 ELKGQLDKLVV 91
ProC COG0345
Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; ...
 1-88 8.41e-09

Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Pyrroline-5-carboxylate reductase is part of the Pathway/BioSystem: Proline biosynthesis


Pssm-ID: 440114 [Multi-domain]  Cd Length: 267  Bit Score: 52.76  E-value: 8.41e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   1 MTTYAIIGAGAIGSALAERFTAAQIPA--IIANSRGPASLSSVTDRFGASVKAVELKDALQADVVILAV-PYDsIADIVT 77
Cdd:COG0345     2 SMKIGFIGAGNMGSAIIKGLLKSGVPPedIIVSDRSPERLEALAERYGVRVTTDNAEAAAQADVVVLAVkPQD-LAEVLE 80

                          90
                  ....*....|...
gi 2179479887  78 QVSDW--GGRIVV 88
Cdd:COG0345    81 ELAPLldPDKLVI 93
PRK14619 PRK14619
NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional
 2-137 7.98e-06

NAD(P)H-dependent glycerol-3-phosphate dehydrogenase; Provisional


Pssm-ID: 237771 [Multi-domain]  Cd Length: 308  Bit Score: 44.21  E-value: 7.98e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   2 TTYAIIGAGAIGSALAERFTAAQIPAIIANSRGPASLSSVtdrfgasvkaveLKDalqADVVILAVPYDSIADIVTQVSD 81
Cdd:PRK14619    5 KTIAILGAGAWGSTLAGLASANGHRVRVWSRRSGLSLAAV------------LAD---ADVIVSAVSMKGVRPVAEQVQA 69

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2179479887  82 WG---GRIVVDASNAID--------------FPAFKPRDLGG-RLSTEIVSELvPGAKVVKAFNTLPAAVLAEI 137
Cdd:PRK14619   70 LNlppETIIVTATKGLDpettrtpsqiwqaaFPNHPVVVLSGpNLSKEIQQGL-PAATVVASRDLAAAETVQQI 142
2-Hacid_dh_C pfam02826
D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; This domain is inserted ...
 3-69 1.98e-05

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: 42.48  E-value: 1.98e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2179479887   3 TYAIIGAGAIGSALAERFTAAQIPaIIANSRGPaSLSSVTDRFGasVKAVELKDAL-QADVVILAVPY 69
Cdd:pfam02826  38 TVGIIGLGRIGRAVAKRLKAFGMK-VIAYDRYP-KPEEEEEELG--ARYVSLDELLaESDVVSLHLPL 101
GpsA COG0240
Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Glycerol-3-phosphate ...
 5-135 9.44e-05

Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Glycerol-3-phosphate dehydrogenase is part of the Pathway/BioSystem: Isoprenoid biosynthesis


Pssm-ID: 440010 [Multi-domain]  Cd Length: 327  Bit Score: 41.18  E-value: 9.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   5 AIIGAGAIGSALAERFT------------AAQIPAIIANSRGPASLSSVtdRFGASVKAV-ELKDALQ-ADVVILAVPYD 70
Cdd:COG0240     4 AVLGAGSWGTALAKVLArnghevtlwgrdPEVAEEINETRENPRYLPGV--KLPENLRATsDLEEALAgADLVLLAVPSQ 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2179479887  71 SIADIVTQVSDW--GGRIVVDASNAIDfpafkpRDLGGRLStEIVSELVPGAkvvkafntLPAAVLA 135
Cdd:COG0240    82 ALREVLEQLAPLlpPGAPVVSATKGIE------PGTGLLMS-EVIAEELPGA--------LRIAVLS 133
TyrA COG0287
Prephenate dehydrogenase [Amino acid transport and metabolism]; Prephenate dehydrogenase is ...
 1-91 1.21e-04

Prephenate dehydrogenase [Amino acid transport and metabolism]; Prephenate dehydrogenase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis


Pssm-ID: 440056 [Multi-domain]  Cd Length: 278  Bit Score: 40.88  E-value: 1.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   1 MTTYAIIGAGAIGSALAERFTAAQIPA-IIANSRGPASLSSVTDRFGASVKAVELKDAL-QADVVILAVPYDSIADIVTQ 78
Cdd:COG0287     1 FMRIAIIGLGLIGGSLALALKRAGLAHeVVGVDRSPETLERALELGVIDRAATDLEEAVaDADLVVLAVPVGATIEVLAE 80

                          90
                  ....*....|....*
gi 2179479887  79 VSDWG--GRIVVDAS 91
Cdd:COG0287    81 LAPHLkpGAIVTDVG 95
2-Hacid_dh_11 cd12175
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ...
 3-69 1.50e-04

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: 40.63  E-value: 1.50e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2179479887   3 TYAIIGAGAIGSALAERFTAAQiPAIIANSRGPASlSSVTDRFGASvkAVELKDALQ-ADVVILAVPY 69
Cdd:cd12175   144 TVGIVGLGNIGRAVARRLRGFG-VEVIYYDRFRDP-EAEEKDLGVR--YVELDELLAeSDVVSLHVPL 207
PanE COG1893
Ketopantoate reductase [Coenzyme transport and metabolism]; Ketopantoate reductase is part of ...
 4-140 2.55e-04

Ketopantoate reductase [Coenzyme transport and metabolism]; Ketopantoate reductase is part of the Pathway/BioSystem: Pantothenate/CoA biosynthesis


Pssm-ID: 441497 [Multi-domain]  Cd Length: 305  Bit Score: 39.84  E-value: 2.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   4 YAIIGAGAIGSALAERFTAA-QIPAIIANSRGPASL--------SSVTDRFGASVKAVELKDAL-QADVVILAVPYDSIA 73
Cdd:COG1893     3 IAILGAGAIGGLLGARLARAgHDVTLVARGAHAEALrenglrleSPDGDRTTVPVPAVTDPEELgPADLVLVAVKAYDLE 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2179479887  74 DIVTQVSDWGGR--IVVDASNAIDfpafkprdlggrlSTEIVSELVPGAKVVKAFNTLPAAVLAEIRIR 140
Cdd:COG1893    83 AAAEALAPLLGPdtVVLSLQNGLG-------------HEERLAEALGAERVLGGVVTIGATREEPGVVR 138
formate_dh_like cd05198
Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase ...
 3-69 2.80e-04

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: 39.92  E-value: 2.80e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2179479887   3 TYAIIGAGAIGSALAERFTAAQIPAIIAN-SRGPASLSSVTDRFgasvkaVELKDAL-QADVVILAVPY 69
Cdd:cd05198   142 TVGIVGLGRIGQRVAKRLQAFGMKVLYYDrTRKPEPEEDLGFRV------VSLDELLaQSDVVVLHLPL 204
SerA COG0111
Phosphoglycerate dehydrogenase or related dehydrogenase [Coenzyme transport and metabolism]; ...
 6-69 3.54e-04

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: 39.41  E-value: 3.54e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2179479887   6 IIGAGAIGSALAERFTAAQIPaIIANSRGPASLSSVTDRFGasvKAVELKDAL-QADVVILAVPY 69
Cdd:COG0111   145 IVGLGRIGRAVARRLRAFGMR-VLAYDPSPKPEEAADLGVG---LVDSLDELLaEADVVSLHLPL 205
PRK08507 PRK08507
prephenate dehydrogenase; Validated
 50-90 3.70e-04

prephenate dehydrogenase; Validated


Pssm-ID: 181452 [Multi-domain]  Cd Length: 275  Bit Score: 39.49  E-value: 3.70e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2179479887  50 KAVELKDALQADVVILAVPYDSIADIVTQVSDWG-GRIVVDA 90
Cdd:PRK08507   49 EIVSFEELKKCDVIFLAIPVDAIIEILPKLLDIKeNTTIIDL 90
2-Hacid_dh_1 cd05300
Putative D-isomer specific 2-hydroxyacid dehydrogenase; 2-Hydroxyacid dehydrogenases catalyze ...
 6-68 4.22e-04

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: 39.43  E-value: 4.22e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2179479887   6 IIGAGAIGSALAERFTA--AQipaIIANSRGPASLSSVTDR-FGASvkavELKDAL-QADVVILAVP 68
Cdd:cd05300   139 IVGLGDIGREIARRAKAfgMR---VIGVRRSGRPAPPVVDEvYTPD----ELDELLpEADYVVNALP 198
Zn_ADH9 cd08269
Alcohol dehydrogenases of the MDR family; The medium chain dehydrogenases/reductase (MDR) ...
 3-88 7.00e-04

Alcohol dehydrogenases of the MDR family; The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P)-binding Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability.


Pssm-ID: 176230 [Multi-domain]  Cd Length: 312  Bit Score: 38.88  E-value: 7.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   3 TYAIIGAGAIGSALAERFTAAQIPAIIANSRGPASLsSVTDRFGA-------SVKAVE----LKDALQADVVILAVPYDS 71
Cdd:cd08269   132 TVAVIGAGFIGLLFLQLAAAAGARRVIAIDRRPARL-ALARELGAtevvtddSEAIVErvreLTGGAGADVVIEAVGHQW 210

                          90
                  ....*....|....*..
gi 2179479887  72 IADIVTQVSDWGGRIVV 88
Cdd:cd08269   211 PLDLAGELVAERGRLVI 227
ASADH_AGPR_N cd02281
N-terminal NAD(P)-binding domain of aspartate-beta-semialdehyde dehydrogenase (ASADH) and ...
 2-97 1.34e-03

N-terminal NAD(P)-binding domain of aspartate-beta-semialdehyde dehydrogenase (ASADH) and N-acetyl-gamma-glutamyl-phosphate reductase (AGPR); Aspartate-beta-semialdehyde dehydrogenase (ASADH, EC 1.2.1.11), also called ASA dehydrogenase (ASD), or aspartate-beta-semialdehyde dehydrogenase, catalyzes the second step of the aspartate biosynthetic pathway, an essential enzyme found in bacteria, fungi, and higher plants. ASADH catalyses the formation of L-aspartate-beta-semialdehyde (ASA) by the reductive dephosphorylation of L-beta-aspartyl phosphate (BAP), utilizing the reducing power of NADPH. ASA can either be further reduced to homoserine, which leads to methionine, threonine, or isoleucine, or it can be condensed with pyruvate and cyclized into dihydrodipicolinate, and then converted into diaminopimelate, a component of bacterial cell walls, and finally decarboxylated to produce lysine. N-acetyl-gamma-glutamyl-phosphate reductase (AGPR, EC 1.2.1.38), also called N-acetyl-glutamate semialdehyde dehydrogenase, or NAGSA dehydrogenase, reversibly catalyses the NADPH-dependent reduction of N-acetyl-gamma-glutamyl phosphate; the third step of arginine biosynthesis. ASADH and AGPR proteins contain an N-terminal Rossmann fold NAD(P)H binding domain and a C-terminal glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like domain.


Pssm-ID: 467516 [Multi-domain]  Cd Length: 145  Bit Score: 36.96  E-value: 1.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   2 TTYAIIGA-GAIGSALAERFTAAQIPAIIANSRGPASLSSVTDRFGAS------VKAVELKDALQADVVILAVPYDSIAD 74
Cdd:cd02281     1 KKVGVVGAtGYVGGEFLRLLLEHPFPLFEIVLLAASSAGAKKKYFHPKlwgrvlVEFTPEEVLEQVDIVFTALPGGVSAK 80

                          90       100
                  ....*....|....*....|....*.
gi 2179479887  75 IVTQVSDWGGRIVVDASN---AIDFP 97
Cdd:cd02281    81 LAPELSEAGVLVIDNASDfrlDKDVP 106
PRK06545 PRK06545
prephenate dehydrogenase; Validated
 6-91 1.72e-03

prephenate dehydrogenase; Validated


Pssm-ID: 235824 [Multi-domain]  Cd Length: 359  Bit Score: 37.58  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   6 IIGAGAIGSALAERFTAAQIPAIIANSRGPASLSSVTDRFGASVKAVEL--KDALQADVVILAVPYDSIADIVTQVSDWG 83
Cdd:PRK06545    5 IVGLGLIGGSLALAIKAAGPDVFIIGYDPSAAQLARALGFGVIDELAADlqRAAAEADLIVLAVPVDATAALLAELADLE 84

                          90
                  ....*....|.
gi 2179479887  84 ---GRIVVDAS 91
Cdd:PRK06545   85 lkpGVIVTDVG 95
MmsB COG2084
3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport ...
 1-91 2.14e-03

3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism];


Pssm-ID: 441687 [Multi-domain]  Cd Length: 285  Bit Score: 37.40  E-value: 2.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   1 MTTYAIIGAGAIGSALAERFTAAQIPAIIANsRGPASLSSVTDRfGASVKAVELKDALQADVVILAVPYDsiaDIVTQV- 79
Cdd:COG2084     1 MMKVGFIGLGAMGAPMARNLLKAGHEVTVWN-RTPAKAEALVAA-GARVAASPAEAAAAADVVITMLPDD---AAVEEVl 75

                          90       100
                  ....*....|....*....|
gi 2179479887  80 -SDWG-------GRIVVDAS 91
Cdd:COG2084    76 lGEDGllaalrpGAVVVDMS 95
NAD_bind_Glutamyl_tRNA_reduct cd05213
NADP-binding domain of glutamyl-tRNA reductase; Glutamyl-tRNA reductase catalyzes the ...
 5-111 2.74e-03

NADP-binding domain of glutamyl-tRNA reductase; Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids to keto acids with NAD(P)+ as a cofactor. The NAD(P)-binding Rossmann fold superfamily includes a wide variety of protein families including NAD(P)- binding domains of alcohol DHs, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate DH, lactate/malate DHs, formate/glycerate DHs, siroheme synthases, 6-phosphogluconate DH, amino acid DHs, repressor rex, NAD-binding potassium channel domain, CoA-binding, and ornithine cyclodeaminase-like domains. These domains have an alpha-beta-alpha configuration. NAD binding involves numerous hydrogen and van der Waals contacts.


Pssm-ID: 133452 [Multi-domain]  Cd Length: 311  Bit Score: 36.86  E-value: 2.74e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   5 AIIGAGAIGSALAERFTAAQIPAI-IANsRGPASLSSVTDRFGAS-VKAVELKDAL-QADVVILAV----PYDSIADIVT 77
Cdd:cd05213   182 LVIGAGEMGELAAKHLAAKGVAEItIAN-RTYERAEELAKELGGNaVPLDELLELLnEADVVISATgaphYAKIVERAMK 260

                          90       100       110
                  ....*....|....*....|....*....|....
gi 2179479887  78 QVSDwGGRIVVDASNaidfpafkPRDLGGRLSTE 111
Cdd:cd05213   261 KRSG-KPRLIVDLAV--------PRDIEPEVGEL 285
2-Hacid_dh_7 cd12166
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ...
 6-69 4.10e-03

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: 36.41  E-value: 4.10e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2179479887   6 IIGAGAIGSALAERFTAAQipaiiansrgpASLSSV--TDRFGASVKAVELKDAL--QADVVILAVPY 69
Cdd:cd12166   137 IVGYGSIGRAIERRLAPFE-----------VRVTRVarTARPGEQVHGIDELPALlpEADVVVLIVPL 193
NAD_Gly3P_dh_N pfam01210
NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent ...
 5-123 4.46e-03

NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus; NAD-dependent glycerol-3-phosphate dehydrogenase (GPDH) catalyzes the interconversion of dihydroxyacetone phosphate and L-glycerol-3-phosphate. This family represents the N-terminal NAD-binding domain.


Pssm-ID: 395967 [Multi-domain]  Cd Length: 158  Bit Score: 35.63  E-value: 4.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   5 AIIGAGAIGSALAERFT------------AAQIPAIIANSRGPASLSSVTdrFGASVKAV-ELKDALQ-ADVVILAVPYD 70
Cdd:pfam01210   3 AVLGAGSWGTALAKVLAdnghevrlwgrdEELIEEINTTHENVRYLPGIK--LPENLKATtDLAEALKgADIIVIVVPSQ 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2179479887  71 SIADIVTQVSDW--GGRIVVDASNAIDfpafkprDLGGRLSTEIVSELVPGAKVV 123
Cdd:pfam01210  81 ALREVLKQLKGLlkPDAILVSLSKGIE-------PGTLKLLSEVIEEELGIQPPI 128
gpsA PRK00094
NAD(P)H-dependent glycerol-3-phosphate dehydrogenase;
1-119 5.33e-03

NAD(P)H-dependent glycerol-3-phosphate dehydrogenase;


Pssm-ID: 234629 [Multi-domain]  Cd Length: 325  Bit Score: 36.20  E-value: 5.33e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2179479887   1 MTTYAIIGAGAIGSALA----ER--------FTAAQIPAIIANSRGPASLSSVTdrFGASVKAV-ELKDALQ-ADVVILA 66
Cdd:PRK00094    1 MMKIAVLGAGSWGTALAivlaRNghdvtlwaRDPEQAAEINADRENPRYLPGIK--LPDNLRATtDLAEALAdADLILVA 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2179479887  67 VPYDSIADIVTQVSDW--GGRIVVDASNAIDfpafkpRDLGGRLStEIVSELVPG 119
Cdd:PRK00094   79 VPSQALREVLKQLKPLlpPDAPIVWATKGIE------PGTGKLLS-EVLEEELPD 126
2-Hacid_dh_6 cd12165
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ...
 3-70 6.75e-03

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: 35.68  E-value: 6.75e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2179479887   3 TYAIIGAGAIGSALAERFTA--AQipaIIANSRGPASLSSVTDRFGASvkavELKDAL-QADVVILAVPYD 70
Cdd:cd12165   139 TVGILGYGHIGREIARLLKAfgMR---VIGVSRSPKEDEGADFVGTLS----DLDEALeQADVVVVALPLT 202
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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