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1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase [Macaca mulatta]

Protein Classification

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase( domain architecture ID 14388757)

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

CATH:  2.60.120.10
EC:  1.13.11.54|1.13.11.53
Gene Ontology:  GO:0019509|GO:0010309|GO:0005506|GO:0010308|GO:0016151
PubMed:  9880484|16989860|14697267|19478949
SCOP:  4002777

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 28-157 1.07e-71

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: 212.40  E-value: 1.07e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966979605  28 LEQLRRLGVLYWKLDADKYEN-----DPELEKIRRERNYSWMDIITICKDKlPNYEEKIKMFYEEHLHLDDEIRYILDGS 102
Cdd:cd02232    1 AEELAELGVLYERWDADDLEAagaayDEELDALKKERGYKSRDVVTLSPET-PNYEEKLKKFFEEHLHEDDEVRFILDGS 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 966979605 103 GYFDVRDKEDKWIRIFMEKGDMITLPAGIYHRFTVDEKNYAKAMRLFVGEPVWTA 157
Cdd:cd02232   80 GYFDVRDKDDEWIRILVEKGDLIVVPAGIYHRFTLDENPYIKAVRLFKDEPGWVP 134
 
Name Accession Description Interval E-value
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 28-157 1.07e-71

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: 212.40  E-value: 1.07e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966979605  28 LEQLRRLGVLYWKLDADKYEN-----DPELEKIRRERNYSWMDIITICKDKlPNYEEKIKMFYEEHLHLDDEIRYILDGS 102
Cdd:cd02232    1 AEELAELGVLYERWDADDLEAagaayDEELDALKKERGYKSRDVVTLSPET-PNYEEKLKKFFEEHLHEDDEVRFILDGS 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 966979605 103 GYFDVRDKEDKWIRIFMEKGDMITLPAGIYHRFTVDEKNYAKAMRLFVGEPVWTA 157
Cdd:cd02232   80 GYFDVRDKDDEWIRILVEKGDLIVVPAGIYHRFTLDENPYIKAVRLFKDEPGWVP 134
ARD pfam03079
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ...
 3-157 2.32e-67

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: 202.59  E-value: 2.32e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966979605    3 QAWYMDDAP-GDPRQPHRPDPDRPVGLEQLRRLGVLYWKLDADKYENDPELEKIRRERNYSWMDII-TICKDKLPNYEEK 80
Cdd:pfam03079   1 RIWIMDDSPcGDQRLPHHTFPKEKAETDELAKLGVLYWKLDADDEETAEDLLRILKYKHYDDVDIDvTVCPETTPNFDEK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 966979605   81 IKMFYEEHLHLDDEIRYILDGSGYFDVRDKEDKWIRIFMEKGDMITLPAGIYHRFTVDEKNYAKAMRLFVGEPVWTA 157
Cdd:pfam03079  81 LEKFFEEHLHTDEEIRYIVEGTGYFDVRDKDDVWIRVFVEKGDLISLPAGIYHRFTTTPDNYVKALRLFVTKPGWTA 157
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
85-154 3.20e-07

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 46.38  E-value: 3.20e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966979605  85 YEEHLHLDDEIRYILDGSGYFDVrdkEDKWIRIfmEKGDMITLPAGIYHRFTVDEKnyAKAMRLFVGEPV 154
Cdd:COG1917   36 TPWHSHPGEELIYVLEGEGEVEV---GGEEYEL--KPGDVVFIPPGVPHAFRNLGD--EPAVLLVVFSPG 98
 
Name Accession Description Interval E-value
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 28-157 1.07e-71

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: 212.40  E-value: 1.07e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966979605  28 LEQLRRLGVLYWKLDADKYEN-----DPELEKIRRERNYSWMDIITICKDKlPNYEEKIKMFYEEHLHLDDEIRYILDGS 102
Cdd:cd02232    1 AEELAELGVLYERWDADDLEAagaayDEELDALKKERGYKSRDVVTLSPET-PNYEEKLKKFFEEHLHEDDEVRFILDGS 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 966979605 103 GYFDVRDKEDKWIRIFMEKGDMITLPAGIYHRFTVDEKNYAKAMRLFVGEPVWTA 157
Cdd:cd02232   80 GYFDVRDKDDEWIRILVEKGDLIVVPAGIYHRFTLDENPYIKAVRLFKDEPGWVP 134
ARD pfam03079
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ...
 3-157 2.32e-67

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: 202.59  E-value: 2.32e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966979605    3 QAWYMDDAP-GDPRQPHRPDPDRPVGLEQLRRLGVLYWKLDADKYENDPELEKIRRERNYSWMDII-TICKDKLPNYEEK 80
Cdd:pfam03079   1 RIWIMDDSPcGDQRLPHHTFPKEKAETDELAKLGVLYWKLDADDEETAEDLLRILKYKHYDDVDIDvTVCPETTPNFDEK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 966979605   81 IKMFYEEHLHLDDEIRYILDGSGYFDVRDKEDKWIRIFMEKGDMITLPAGIYHRFTVDEKNYAKAMRLFVGEPVWTA 157
Cdd:pfam03079  81 LEKFFEEHLHTDEEIRYIVEGTGYFDVRDKDDVWIRVFVEKGDLISLPAGIYHRFTTTPDNYVKALRLFVTKPGWTA 157
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
85-154 3.20e-07

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 46.38  E-value: 3.20e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 966979605  85 YEEHLHLDDEIRYILDGSGYFDVrdkEDKWIRIfmEKGDMITLPAGIYHRFTVDEKnyAKAMRLFVGEPV 154
Cdd:COG1917   36 TPWHSHPGEELIYVLEGEGEVEV---GGEEYEL--KPGDVVFIPPGVPHAFRNLGD--EPAVLLVVFSPG 98
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 86-135 4.01e-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: 42.63  E-value: 4.01e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 966979605   86 EEHLH-LDDEIRYILDGSGYFDVRDKEdkwirIFMEKGDMITLPAGIYHRF 135
Cdd:pfam07883  12 PPHRHpGEDEFFYVLEGEGELTVDGEE-----VVLKAGDSVYFPAGVPHRF 57
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 87-144 1.01e-05

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: 41.70  E-value: 1.01e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 966979605  87 EHLH-LDDEIRYILDGSGYFDVRDKEdkwiRIFMEKGDMITLPAGIYHRFTVDEKNYAK 144
Cdd:cd02208   14 PHWHpEQDEIFYVLSGEGELTLDDGE----TVELKAGDIVLIPPGVPHSFVNTSDEPAV 68
OxdD COG2140
Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate ...
 86-135 7.04e-05

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: 40.33  E-value: 7.04e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 966979605  86 EEHLHLD-DEIRYILDGSGYFDVRDKEDKWIRIFMEKGDMITLPAGIYHRF 135
Cdd:COG2140   17 EEHWHPNaAEWYYVLSGEARMTVQDPPGRARTVDVGPGDVVYVPPGYGHYI 67
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
85-135 7.34e-05

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 40.51  E-value: 7.34e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 966979605  85 YEEHLHLD-DEIRYILDGSGYFDVRDKEdkwirIFMEKGDMITLPAGIYHRF 135
Cdd:COG0662   40 LSLHVHPHrDEFFYVLEGTGEVTIGDEE-----VELKAGDSVYIPAGVPHRL 86
AraC_binding pfam02311
AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization ...
 85-157 4.88e-04

AraC-like ligand binding domain; This family represents the arabinose-binding and dimerization domain of the bacterial gene regulatory protein AraC. The domain is found in conjunction with the helix-turn-helix (HTH) DNA-binding motif pfam00165. This domain is distantly related to the Cupin domain pfam00190.


Pssm-ID: 396749 [Multi-domain]  Cd Length: 134  Bit Score: 38.57  E-value: 4.88e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 966979605   85 YEEHLHLDDEIRYILDGSGYFDVRDKedkwiRIFMEKGDMITLPAGIYHRFTVD-EKNYAKAMRLFVGEPVWTA 157
Cdd:pfam02311  16 FPPHVHDFYVIGYIERGVGRFRLNGR-----TYHLGPGDLFLLPPGEPHDYEPEsEDGWRYRWLYFEPELLERI 84
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
88-135 1.32e-03

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 36.92  E-value: 1.32e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 966979605  88 HLHLD-DEIRYILDGSGYFDVRDKEdkwirIFMEKGDMITLPAGIYHRF 135
Cdd:COG3837   45 HAHSAeEEFVYVLEGELTLRIGGEE-----YVLEPGDSVGFPAGVPHRL 88
cupin_GDO-like_N cd02216
gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, ...
 88-133 7.02e-03

gentisate 1,2-dioxygenase, 1-hydroxy-2-naphthoate dioxygenase, and salicylate 1,2-dioxygenase, N-terminal cupin domain; This family includes the N-terminal cupin domains of three closely related bicupin aromatic ring-cleaving dioxygenases: gentisate 1,2-dioxygenase (GDO), salicylate 1,2-dioxygenase (SDO), and 1-hydroxy-2-naphthoate dioxygenase (NDO). GDO catalyzes the cleavage of the gentisate (2,5-dihydroxybenzoate) aromatic ring, a key step in the gentisate degradation pathway allowing soil bacteria to utilize 2,5-xylenol, 3,5-xylenol, and m-cresol as sole carbon and energy sources. NDO catalyzes the cleavage of 1-hydroxy-2-naphthoate as part of the bacterial phenanthrene degradation pathway. SDO is a ring cleavage dioxygenase from Pseudaminobacter salicylatoxidans that oxidizes salicylate to 2-oxohepta-3,5-dienedioic acid via a novel ring fission mechanism. SDO differs from other known GDOs and NDOs in its unique ability to oxidatively cleave many different salicylate, gentisate and 1-hydroxy-2-naphthoate substrates with high catalytic efficiency. The active site of these enzymes is located in the N-terminal domain but could be influenced by changes in the C-terminal domain, which lacks the strictly conserved metal-binding residues found in other cupin domains and is thought to be an inactive vestigial remnant.


Pssm-ID: 380346 [Multi-domain]  Cd Length: 108  Bit Score: 34.84  E-value: 7.02e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 966979605  88 HLHLDDEIRYILDGSGYFDVRDKEdkwiRIFMEKGDMITLPAGIYH 133
Cdd:cd02216   37 HRHTPNALRFVLEGPGAYTTVDGE----RCDMEPGDLILTPPGTWH 78
 
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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