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Conserved domains on  [gi|488387849|ref|WP_002457234|]
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glyoxalase [Staphylococcus epidermidis]

Protein Classification

VOC family protein( domain architecture ID 50733)

vicinal oxygen chelate (VOC) family protein uses a metal center to coordinate a substrate, intermediate, or transition state through vicinal oxygen atoms

CATH:  3.10.180.10
Gene Ontology:  GO:0046872|GO:0003824
PubMed:  21820381|11076500

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PhnB super family cl42691
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
14-119 2.30e-06

Zn-dependent glyoxalase, PhnB family [Energy production and conversion];


The actual alignment was detected with superfamily member COG2764:

Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 43.69  E-value: 2.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849  14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEHLRLAKYQdIMLIS---GKQFEVGNAVYTNILVPNIRILKQRISSQ- 89
Cdd:COG2764    8 VDDAEEALEFYEDVFGFEVVFRMTDPDGKIMHAELRIGGSV-LMLSDappDSPAAEGNGVSLSLYVDDVDALFARLVAAg 86

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488387849  90 -YIVEDLEEKPWNSIEMTIKDLDNHLITLTQ 119
Cdd:COG2764   87 aTVVMPLQDTFWGDRFGMVRDPFGVLWMINT 117
 
Name Accession Description Interval E-value
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
14-119 2.30e-06

Zn-dependent glyoxalase, PhnB family [Energy production and conversion];


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 43.69  E-value: 2.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849  14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEHLRLAKYQdIMLIS---GKQFEVGNAVYTNILVPNIRILKQRISSQ- 89
Cdd:COG2764    8 VDDAEEALEFYEDVFGFEVVFRMTDPDGKIMHAELRIGGSV-LMLSDappDSPAAEGNGVSLSLYVDDVDALFARLVAAg 86

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488387849  90 -YIVEDLEEKPWNSIEMTIKDLDNHLITLTQ 119
Cdd:COG2764   87 aTVVMPLQDTFWGDRFGMVRDPFGVLWMINT 117
BLMA_like cd08349
Bleomycin binding protein (BLMA) and similar proteins; BLMA also called Bleomycin resistance ...
 14-119 1.20e-05

Bleomycin binding protein (BLMA) and similar proteins; BLMA also called Bleomycin resistance protein, confers Bm resistance by directly binding to Bm. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMA is produced by actinomycetes to protect themselves against their own lethal compound. BLMA has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMAs are dimers and each dimer binds to two Bm molecules at the Bm-binding pockets formed at the dimer interface; two Bm molecules are bound per dimer. BLMA belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. As for the larger superfamily, this family contains members with or without domain swapping.


Pssm-ID: 319937 [Multi-domain]  Cd Length: 114  Bit Score: 41.83  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849  14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEH---LRLAKYQDImlisgKQFEVGNAVYtnILVPNIRILKQRISSQ- 89
Cdd:cd08349    6 VRDIDKTLAFYVDVLGFEVDYERPPPGYAILSRGgveLHLFEHPGL-----DPAGSGVAAY--IRVEDIDALHAELKAAg 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488387849  90 ------YIVEDLEEKPWNSIEMTIKDLDNHLITLTQ 119
Cdd:cd08349   79 lplfgiPRITPIEDKPWGMREFAVVDPDGNLLRFGQ 114
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
14-115 2.83e-03

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 35.50  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849   14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEHLRLAKYQDIMLIS-------GKQFEVGNAVYTNILVPNIRILKQRI 86
Cdd:pfam00903   9 VGDLEKSLDFYTDVLGFKLVEETDAGEEGGLRSAFFLAGGRVLELLLnetpppaAAGFGGHHIAFIAFSVDDVDAAYDRL 88

                          90       100       110
                  ....*....|....*....|....*....|.
gi 488387849   87 SSQ--YIVEDLEEKPWNSIEMTIKDLDNHLI 115
Cdd:pfam00903  89 KAAgvEIVREPGRHGWGGRYSYFRDPDGNLI 119
 
Name Accession Description Interval E-value
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
14-119 2.30e-06

Zn-dependent glyoxalase, PhnB family [Energy production and conversion];


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 43.69  E-value: 2.30e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849  14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEHLRLAKYQdIMLIS---GKQFEVGNAVYTNILVPNIRILKQRISSQ- 89
Cdd:COG2764    8 VDDAEEALEFYEDVFGFEVVFRMTDPDGKIMHAELRIGGSV-LMLSDappDSPAAEGNGVSLSLYVDDVDALFARLVAAg 86

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488387849  90 -YIVEDLEEKPWNSIEMTIKDLDNHLITLTQ 119
Cdd:COG2764   87 aTVVMPLQDTFWGDRFGMVRDPFGVLWMINT 117
BLMA_like cd08349
Bleomycin binding protein (BLMA) and similar proteins; BLMA also called Bleomycin resistance ...
 14-119 1.20e-05

Bleomycin binding protein (BLMA) and similar proteins; BLMA also called Bleomycin resistance protein, confers Bm resistance by directly binding to Bm. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMA is produced by actinomycetes to protect themselves against their own lethal compound. BLMA has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMAs are dimers and each dimer binds to two Bm molecules at the Bm-binding pockets formed at the dimer interface; two Bm molecules are bound per dimer. BLMA belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. As for the larger superfamily, this family contains members with or without domain swapping.


Pssm-ID: 319937 [Multi-domain]  Cd Length: 114  Bit Score: 41.83  E-value: 1.20e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849  14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEH---LRLAKYQDImlisgKQFEVGNAVYtnILVPNIRILKQRISSQ- 89
Cdd:cd08349    6 VRDIDKTLAFYVDVLGFEVDYERPPPGYAILSRGgveLHLFEHPGL-----DPAGSGVAAY--IRVEDIDALHAELKAAg 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488387849  90 ------YIVEDLEEKPWNSIEMTIKDLDNHLITLTQ 119
Cdd:cd08349   79 lplfgiPRITPIEDKPWGMREFAVVDPDGNLLRFGQ 114
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 14-117 2.44e-05

vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases.


Pssm-ID: 319898 [Multi-domain]  Cd Length: 112  Bit Score: 40.97  E-value: 2.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849  14 VNDIEKSSEWYQENLGFKSIFKFKNEQNqilmEHLRLAKYQDIMLISGKQFEVGNAVYTN---ILVPNI----RILKQRI 86
Cdd:cd06587    6 VPDLDASVAFYEEVLGFEVVSRNEGGGF----AFLRLGPGLRLALLEGPEPERPGGGGLFhlaFEVDDVdevdERLREAG 81

                         90       100       110
                 ....*....|....*....|....*....|.
gi 488387849  87 SSQYIVEDLEEKPWNSIEMTIKDLDNHLITL 117
Cdd:cd06587   82 AEGELVAPPVDDPWGGRSFYFRDPDGNLIEF 112
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 14-119 1.05e-04

Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 440115 [Multi-domain]  Cd Length: 125  Bit Score: 39.21  E-value: 1.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849  14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEHLRLAKYQDIMLIS----GKQFEVGNAVYTNILVPNIRILKQRISSQ 89
Cdd:COG0346   10 VSDLEASLAFYTDVLGLELVKRTDFGDGGFGHAFLRLGDGTELELFEapgaAPAPGGGGLHHLAFRVDDLDAAYARLRAA 89

                         90       100       110
                 ....*....|....*....|....*....|..
gi 488387849  90 --YIVEDLEEKPWNSIEMTIKDLDNHLITLTQ 119
Cdd:COG0346   90 gvEIEGEPRDRAYGYRSAYFRDPDGNLIELVE 121
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
14-115 2.83e-03

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 35.50  E-value: 2.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488387849   14 VNDIEKSSEWYQENLGFKSIFKFKNEQNQILMEHLRLAKYQDIMLIS-------GKQFEVGNAVYTNILVPNIRILKQRI 86
Cdd:pfam00903   9 VGDLEKSLDFYTDVLGFKLVEETDAGEEGGLRSAFFLAGGRVLELLLnetpppaAAGFGGHHIAFIAFSVDDVDAAYDRL 88

                          90       100       110
                  ....*....|....*....|....*....|.
gi 488387849   87 SSQ--YIVEDLEEKPWNSIEMTIKDLDNHLI 115
Cdd:pfam00903  89 KAAgvEIVREPGRHGWGGRYSYFRDPDGNLI 119
 
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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