acireductone dioxygenase [Streptomyces hokutonensis]
Protein Classification
1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase( domain architecture ID 10004526)
1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase, also called acireductone dioxygenase, catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| Adi1 | COG1791 | Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and ... |
1-186 | 8.62e-94 | ||||
Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism]; : Pssm-ID: 441396 Cd Length: 180 Bit Score: 270.91 E-value: 8.62e-94
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| Name | Accession | Description | Interval | E-value | ||||
| Adi1 | COG1791 | Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and ... |
1-186 | 8.62e-94 | ||||
Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism]; Pssm-ID: 441396 Cd Length: 180 Bit Score: 270.91 E-value: 8.62e-94
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| cupin_ARD | cd02232 | acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ... |
26-171 | 7.54e-54 | ||||
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization Pssm-ID: 380360 Cd Length: 134 Bit Score: 168.10 E-value: 7.54e-54
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| ARD | pfam03079 | ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ... |
20-170 | 1.88e-28 | ||||
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized. Pssm-ID: 281122 Cd Length: 157 Bit Score: 103.97 E-value: 1.88e-28
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| Cupin_1 | smart00835 | Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' ... |
102-163 | 2.08e-03 | ||||
Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. Pssm-ID: 214845 [Multi-domain] Cd Length: 146 Bit Score: 36.87 E-value: 2.08e-03
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| Name | Accession | Description | Interval | E-value | ||||
| Adi1 | COG1791 | Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and ... |
1-186 | 8.62e-94 | ||||
Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism]; Pssm-ID: 441396 Cd Length: 180 Bit Score: 270.91 E-value: 8.62e-94
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| cupin_ARD | cd02232 | acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ... |
26-171 | 7.54e-54 | ||||
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization Pssm-ID: 380360 Cd Length: 134 Bit Score: 168.10 E-value: 7.54e-54
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| ARD | pfam03079 | ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ... |
20-170 | 1.88e-28 | ||||
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized. Pssm-ID: 281122 Cd Length: 157 Bit Score: 103.97 E-value: 1.88e-28
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| Cupin_2 | pfam07883 | Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ... |
100-156 | 1.75e-06 | ||||
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). Pssm-ID: 462300 [Multi-domain] Cd Length: 71 Bit Score: 44.17 E-value: 1.75e-06
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| ManC | COG0662 | Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism]; |
99-156 | 2.54e-05 | ||||
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism]; Pssm-ID: 440426 [Multi-domain] Cd Length: 114 Bit Score: 42.05 E-value: 2.54e-05
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| cupin_MJ1618 | cd02214 | Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ... |
79-148 | 8.35e-05 | ||||
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. Pssm-ID: 380344 [Multi-domain] Cd Length: 100 Bit Score: 40.19 E-value: 8.35e-05
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| cupin_TcmJ-like | cd06991 | TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of ... |
94-157 | 1.24e-04 | ||||
TcmJ monooxygenase and related proteins, cupin domain; This family includes TcmJ, a subunit of the tetracenomycin (TCM) polyketide synthase (PKS) type II complex in Streptomyces glaucescens. TcmJ is a quinone-forming monooxygenase involved in the modification of aromatic polyketides synthesized by polyketide synthases of types II and III. Orthologs of TcmJ include the Streptomyces BenD (benastatin biosynthetic pathway), the Streptomyces olivaceus ElmJ (polyketide antibiotic elloramycin biosynthetic pathway), the Actinomadura hibisca PdmL (pradimicin biosynthetic pathway), the Streptomyces cyaneus CurC (curamycin biosynthetic pathway), the Streptomyces rishiriensis Lct30 (lactonamycin biosynthetic pathway), and the Streptomyces WhiE II (spore pigment polyketide biosynthetic pathway). Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization. Pssm-ID: 380396 [Multi-domain] Cd Length: 105 Bit Score: 39.58 E-value: 1.24e-04
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| OxdD | COG2140 | Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate ... |
100-149 | 2.90e-04 | ||||
Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate transport and metabolism]; Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily is part of the Pathway/BioSystem: Glycolysis Pssm-ID: 441743 [Multi-domain] Cd Length: 115 Bit Score: 38.79 E-value: 2.90e-04
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| cupin_BF4112 | cd06985 | Bacteroides fragilis BF4112 and related proteins, cupin domain; This family includes archaeal ... |
91-155 | 5.55e-04 | ||||
Bacteroides fragilis BF4112 and related proteins, cupin domain; This family includes archaeal and bacterial proteins homologous to BF4112, a Bacteroides fragilis protein of unknown function. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization. Pssm-ID: 380390 [Multi-domain] Cd Length: 101 Bit Score: 37.89 E-value: 5.55e-04
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| cupin_RmlC-like | cd02208 | RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ... |
101-163 | 1.20e-03 | ||||
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation. Pssm-ID: 380338 [Multi-domain] Cd Length: 73 Bit Score: 36.31 E-value: 1.20e-03
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| CC3_like_SDR_a | cd05250 | CC3(TIP30)-like, atypical (a) SDRs; Atypical SDRs in this subgroup include CC3 (also known as ... |
15-130 | 1.86e-03 | ||||
CC3(TIP30)-like, atypical (a) SDRs; Atypical SDRs in this subgroup include CC3 (also known as TIP30) which is implicated in tumor suppression. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine rich NAD(P)-binding motif that resembles the extended SDRs, and have an active site triad of the SDRs (YXXXK and upstream Ser), although the upstream Asn of the usual SDR active site is substituted with Asp. For CC3, the Tyr of the triad is displaced compared to the usual SDRs and the protein is monomeric, both these observations suggest that the usual SDR catalytic activity is not present. NADP appears to serve an important role as a ligand, and may be important in the interaction with other macromolecules. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Pssm-ID: 187560 [Multi-domain] Cd Length: 214 Bit Score: 37.66 E-value: 1.86e-03
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| COG3837 | COG3837 | Uncharacterized conserved protein, cupin superfamily [Function unknown]; |
91-149 | 1.93e-03 | ||||
Uncharacterized conserved protein, cupin superfamily [Function unknown]; Pssm-ID: 443048 [Multi-domain] Cd Length: 115 Bit Score: 36.53 E-value: 1.93e-03
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| Cupin_1 | smart00835 | Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' ... |
102-163 | 2.08e-03 | ||||
Cupin; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel). This family contains 11S and 7S plant seed storage proteins, and germins. Plant seed storage proteins provide the major nitrogen source for the developing plant. Pssm-ID: 214845 [Multi-domain] Cd Length: 146 Bit Score: 36.87 E-value: 2.08e-03
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| cupin_Pac13-like | cd20295 | monomeric dehydratase Pac13 and related proteins, cupin domain; This family includes a small ... |
100-147 | 2.98e-03 | ||||
monomeric dehydratase Pac13 and related proteins, cupin domain; This family includes a small monomeric dehydratase Pac13 that mediates the formation of the 3'-deoxynucleotide of pacidamycins, which are uradyl peptide antibiotics (UPAs). Pac13 is involved in the formation of the unique 3'-deoxyuridine moiety found in these UPAs; it catalyzes the dehydration of uridine-5'-aldehyde. The similarity of the 3'-deoxy pacidamycin moiety with synthetic anti-retrovirals, offers a potential opportunity for the utilization of Pac13 in the biocatalytic generation of antiviral compounds. Proteins in this family belong to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization. Pssm-ID: 380429 [Multi-domain] Cd Length: 101 Bit Score: 35.66 E-value: 2.98e-03
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| QdoI | COG1917 | Cupin domain protein related to quercetin dioxygenase [General function prediction only]; |
91-164 | 3.69e-03 | ||||
Cupin domain protein related to quercetin dioxygenase [General function prediction only]; Pssm-ID: 441521 [Multi-domain] Cd Length: 99 Bit Score: 35.59 E-value: 3.69e-03
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| cupin_TM1459-like | cd02222 | Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ... |
102-149 | 8.70e-03 | ||||
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer. Pssm-ID: 380351 [Multi-domain] Cd Length: 91 Bit Score: 34.35 E-value: 8.70e-03
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| cupin_TM1287-like | cd02221 | Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial ... |
101-147 | 9.18e-03 | ||||
Thermotoga maritima TM1287 decarboxylase, cupin domain; This family includes bacterial proteins homologous to TM1287 decarboxylase, a Thermotoga maritima manganese-containing cupin thought to catalyze the conversion of oxalate to formate and carbon dioxide, due to its similarity to oxalate decarboxylase (OXDC) from Bacillus subtilis. TM1287 shows a cupin fold with a conserved "jelly roll-like" beta-barrel fold and forms a homodimer. Pssm-ID: 380350 [Multi-domain] Cd Length: 93 Bit Score: 34.37 E-value: 9.18e-03
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