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Conserved domains on  [gi|12655217|gb|AAH01467|]
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Acireductone dioxygenase 1 [Homo sapiens]

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 4.53e-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: 210.86  E-value: 4.53e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12655217  28 LEQLRRLGVLYWKLDADKYEN-----DPELEKIRRERNYSWMDIITICKDKlPNYEEKIKMFYEEHLHLDDEIRYILDGS 102
Cdd:cd02232   1 AEELAELGVLYERWDADDLEAagaayDEELDALKKERGYKSRDVVTLSPET-PNYEEKLKKFFEEHLHEDDEVRFILDGS 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 12655217 103 GYFDVRDKEDQWIRIFMEKGDMVTLPAGIYHRFTVDEKNYTKAMRLFVGEPVWTA 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 4.53e-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: 210.86  E-value: 4.53e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12655217  28 LEQLRRLGVLYWKLDADKYEN-----DPELEKIRRERNYSWMDIITICKDKlPNYEEKIKMFYEEHLHLDDEIRYILDGS 102
Cdd:cd02232   1 AEELAELGVLYERWDADDLEAagaayDEELDALKKERGYKSRDVVTLSPET-PNYEEKLKKFFEEHLHEDDEVRFILDGS 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 12655217 103 GYFDVRDKEDQWIRIFMEKGDMVTLPAGIYHRFTVDEKNYTKAMRLFVGEPVWTA 157
Cdd:cd02232  80 GYFDVRDKDDEWIRILVEKGDLIVVPAGIYHRFTLDENPYIKAVRLFKDEPGWVP 134
ARD pfam03079
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ...
 3-157 2.84e-68

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: 204.90  E-value: 2.84e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12655217     3 QAWYMDDAP-GDPRQPHRPDPGRPVGLEQLRRLGVLYWKLDADKYENDPELEKIRRERNYSWMDII-TICKDKLPNYEEK 80
Cdd:pfam03079   1 RIWIMDDSPcGDQRLPHHTFPKEKAETDELAKLGVLYWKLDADDEETAEDLLRILKYKHYDDVDIDvTVCPETTPNFDEK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 12655217    81 IKMFYEEHLHLDDEIRYILDGSGYFDVRDKEDQWIRIFMEKGDMVTLPAGIYHRFTVDEKNYTKAMRLFVGEPVWTA 157
Cdd:pfam03079  81 LEKFFEEHLHTDEEIRYIVEGTGYFDVRDKDDVWIRVFVEKGDLISLPAGIYHRFTTTPDNYVKALRLFVTKPGWTA 157
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
85-154 3.37e-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: 3.37e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12655217  85 YEEHLHLDDEIRYILDGSGYFDVrdkEDQWIRIfmEKGDMVTLPAGIYHRFTVDEKnyTKAMRLFVGEPV 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 4.53e-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: 210.86  E-value: 4.53e-71
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12655217  28 LEQLRRLGVLYWKLDADKYEN-----DPELEKIRRERNYSWMDIITICKDKlPNYEEKIKMFYEEHLHLDDEIRYILDGS 102
Cdd:cd02232   1 AEELAELGVLYERWDADDLEAagaayDEELDALKKERGYKSRDVVTLSPET-PNYEEKLKKFFEEHLHEDDEVRFILDGS 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*
gi 12655217 103 GYFDVRDKEDQWIRIFMEKGDMVTLPAGIYHRFTVDEKNYTKAMRLFVGEPVWTA 157
Cdd:cd02232  80 GYFDVRDKDDEWIRILVEKGDLIVVPAGIYHRFTLDENPYIKAVRLFKDEPGWVP 134
ARD pfam03079
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ...
 3-157 2.84e-68

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: 204.90  E-value: 2.84e-68
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12655217     3 QAWYMDDAP-GDPRQPHRPDPGRPVGLEQLRRLGVLYWKLDADKYENDPELEKIRRERNYSWMDII-TICKDKLPNYEEK 80
Cdd:pfam03079   1 RIWIMDDSPcGDQRLPHHTFPKEKAETDELAKLGVLYWKLDADDEETAEDLLRILKYKHYDDVDIDvTVCPETTPNFDEK 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 12655217    81 IKMFYEEHLHLDDEIRYILDGSGYFDVRDKEDQWIRIFMEKGDMVTLPAGIYHRFTVDEKNYTKAMRLFVGEPVWTA 157
Cdd:pfam03079  81 LEKFFEEHLHTDEEIRYIVEGTGYFDVRDKDDVWIRVFVEKGDLISLPAGIYHRFTTTPDNYVKALRLFVTKPGWTA 157
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
85-154 3.37e-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: 3.37e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 12655217  85 YEEHLHLDDEIRYILDGSGYFDVrdkEDQWIRIfmEKGDMVTLPAGIYHRFTVDEKnyTKAMRLFVGEPV 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 6.30e-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: 42.25  E-value: 6.30e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 12655217    86 EEHLH-LDDEIRYILDGSGYFDVRDKEdqwirIFMEKGDMVTLPAGIYHRF 135
Cdd:pfam07883  12 PPHRHpGEDEFFYVLEGEGELTVDGEE-----VVLKAGDSVYFPAGVPHRF 57
OxdD COG2140
Oxalate decarboxylase/archaeal phosphoglucose isomerase, cupin superfamily [Carbohydrate ...
 86-135 1.77e-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: 41.88  E-value: 1.77e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 12655217  86 EEHLHLD-DEIRYILDGSGYFDVRDKEDQWIRIFMEKGDMVTLPAGIYHRF 135
Cdd:COG2140  17 EEHWHPNaAEWYYVLSGEARMTVQDPPGRARTVDVGPGDVVYVPPGYGHYI 67
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 87-144 2.96e-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: 40.54  E-value: 2.96e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 12655217  87 EHLH-LDDEIRYILDGSGYFDVRDKEdqwiRIFMEKGDMVTLPAGIYHRFTVDEKNYTK 144
Cdd:cd02208  14 PHWHpEQDEIFYVLSGEGELTLDDGE----TVELKAGDIVLIPPGVPHSFVNTSDEPAV 68
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
85-135 9.73e-05

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


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 40.12  E-value: 9.73e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 12655217  85 YEEHLHLD-DEIRYILDGSGYFDVRDKEdqwirIFMEKGDMVTLPAGIYHRF 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 9.63e-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: 37.41  E-value: 9.63e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 12655217    85 YEEHLHLDDEIRYILDGSGYFDVRDKedqwiRIFMEKGDMVTLPAGIYHRFTVD-EKNYTKAMRLFVGEPVWTA 157
Cdd:pfam02311  16 FPPHVHDFYVIGYIERGVGRFRLNGR-----TYHLGPGDLFLLPPGEPHDYEPEsEDGWRYRWLYFEPELLERI 84
COG3837 COG3837
Uncharacterized conserved protein, cupin superfamily [Function unknown];
88-135 2.04e-03

Uncharacterized conserved protein, cupin superfamily [Function unknown];


Pssm-ID: 443048 [Multi-domain]  Cd Length: 115  Bit Score: 36.15  E-value: 2.04e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 12655217  88 HLHLD-DEIRYILDGSGYFDVRDKEdqwirIFMEKGDMVTLPAGIYHRF 135
Cdd:COG3837  45 HAHSAeEEFVYVLEGELTLRIGGEE-----YVLEPGDSVGFPAGVPHRL 88
 
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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