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Conserved domains on  [gi|1005575881|ref|WP_061668100|]
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MULTISPECIES: VOC family protein [Bacillus]

Protein Classification

VOC family protein( domain architecture ID 10170093)

vicinal oxygen chelate (VOC) family protein similar to Escherichia coli YaeR protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VOC_Bs_YwkD_like cd08352
vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; ...
 4-127 2.98e-72

vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; uncharacterized subfamily of vicinal oxygen chelate (VOC) family contains Bacillus subtilis YwkD and similar proteins. 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


:

Pssm-ID: 319940 [Multi-domain]  Cd Length: 123  Bit Score: 211.25  E-value: 2.98e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   4 SRVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEeYQIELFSFPNPPERKSFPEATGLRHLAFAVT 83
Cdd:cd08352     1 KKIHHIAIICSDYEKSKDFYVDKLGFEIIREHYRPERNDIKLDLALGG-YQLELFIKPDAPARPSYPEALGLRHLAFKVE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1005575881  84 NIEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:cd08352    80 DVEATVAELKSLGIETEPIRVDDFTGKKFTFFFDPDGLPLELYE 123
 
Name Accession Description Interval E-value
VOC_Bs_YwkD_like cd08352
vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; ...
 4-127 2.98e-72

vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; uncharacterized subfamily of vicinal oxygen chelate (VOC) family contains Bacillus subtilis YwkD and similar proteins. 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319940 [Multi-domain]  Cd Length: 123  Bit Score: 211.25  E-value: 2.98e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   4 SRVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEeYQIELFSFPNPPERKSFPEATGLRHLAFAVT 83
Cdd:cd08352     1 KKIHHIAIICSDYEKSKDFYVDKLGFEIIREHYRPERNDIKLDLALGG-YQLELFIKPDAPARPSYPEALGLRHLAFKVE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1005575881  84 NIEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:cd08352    80 DVEATVAELKSLGIETEPIRVDDFTGKKFTFFFDPDGLPLELYE 123
PRK11478 PRK11478
VOC family protein;
1-127 8.45e-62

VOC family protein;


Pssm-ID: 183156 [Multi-domain]  Cd Length: 129  Bit Score: 185.10  E-value: 8.45e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   1 MNISRVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYQIELFSFPNPPERKSFPEATGLRHLAF 80
Cdd:PRK11478    2 LGLKQVHHIAIIATDYAVSKAFYCDILGFTLQSEVYREARDSWKGDLALNGQYVIELFSFPFPPERPSRPEACGLRHLAF 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1005575881  81 AVTNIEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:PRK11478   82 SVDDIDAAVAHLESHNVKCEAIRVDPYTQKRFTFFNDPDGLPLELYE 128
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 5-127 2.70e-37

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: 122.79  E-value: 2.70e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYQIELFSFPNPPerkSFPEATGLRHLAFAVTN 84
Cdd:COG0346     2 GLHHVTLRVSDLEASLAFYTDVLGLELVKRTDFGDGGFGHAFLRLGDGTELELFEAPGAA---PAPGGGGLHHLAFRVDD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1005575881  85 IEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:COG0346    79 LDAAYARLRAAGVEIEGEPRDRAYGYRSAYFRDPDGNLIELVE 121
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
5-125 8.94e-25

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 90.97  E-value: 8.94e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYQIELFSFPNPPERKSFPEATGLRHLAFAVTN 84
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVEETDAGEEGGLRSAFFLAGGRVLELLLNETPPPAAAGFGGHHIAFIAFSVDD 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1005575881  85 IEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLEL 125
Cdd:pfam00903  81 VDAAYDRLKAAGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
metmalonyl_epim TIGR03081
methylmalonyl-CoA epimerase; Members of this protein family are the enzyme methylmalonyl-CoA ...
 5-127 1.36e-08

methylmalonyl-CoA epimerase; Members of this protein family are the enzyme methylmalonyl-CoA epimerase (EC 5.1.99.1), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (TIGR00642). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (TIGR00068), which is also called glyoxylase I, and is also a homodimer.


Pssm-ID: 213772 [Multi-domain]  Cd Length: 128  Bit Score: 49.63  E-value: 1.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYqIELFsfpNPPERKS----FPEAT--GLRHL 78
Cdd:TIGR03081   1 RIDHVGIAVPDLEEAAKFYEDVLGAQVSEIEELPEQGVKVVFIALGNTK-VELL---EPLGEDSpiakFLEKNggGIHHI 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1005575881  79 AFAVTNIEEAVKHLNQCGVKtepiRIDEIT-----GKKFVFF--QDPDGLPLELYE 127
Cdd:TIGR03081  77 AIEVDDIEAALETLKEKGVR----LIDEEPrigahGKPVAFLhpKSTGGVLIELEQ 128
 
Name Accession Description Interval E-value
VOC_Bs_YwkD_like cd08352
vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; ...
 4-127 2.98e-72

vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; uncharacterized subfamily of vicinal oxygen chelate (VOC) family contains Bacillus subtilis YwkD and similar proteins. 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319940 [Multi-domain]  Cd Length: 123  Bit Score: 211.25  E-value: 2.98e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   4 SRVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEeYQIELFSFPNPPERKSFPEATGLRHLAFAVT 83
Cdd:cd08352     1 KKIHHIAIICSDYEKSKDFYVDKLGFEIIREHYRPERNDIKLDLALGG-YQLELFIKPDAPARPSYPEALGLRHLAFKVE 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1005575881  84 NIEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:cd08352    80 DVEATVAELKSLGIETEPIRVDDFTGKKFTFFFDPDGLPLELYE 123
PRK11478 PRK11478
VOC family protein;
1-127 8.45e-62

VOC family protein;


Pssm-ID: 183156 [Multi-domain]  Cd Length: 129  Bit Score: 185.10  E-value: 8.45e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   1 MNISRVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYQIELFSFPNPPERKSFPEATGLRHLAF 80
Cdd:PRK11478    2 LGLKQVHHIAIIATDYAVSKAFYCDILGFTLQSEVYREARDSWKGDLALNGQYVIELFSFPFPPERPSRPEACGLRHLAF 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1005575881  81 AVTNIEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:PRK11478   82 SVDDIDAAVAHLESHNVKCEAIRVDPYTQKRFTFFNDPDGLPLELYE 128
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 5-127 2.70e-37

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: 122.79  E-value: 2.70e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYQIELFSFPNPPerkSFPEATGLRHLAFAVTN 84
Cdd:COG0346     2 GLHHVTLRVSDLEASLAFYTDVLGLELVKRTDFGDGGFGHAFLRLGDGTELELFEAPGAA---PAPGGGGLHHLAFRVDD 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1005575881  85 IEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:COG0346    79 LDAAYARLRAAGVEIEGEPRDRAYGYRSAYFRDPDGNLIELVE 121
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
5-125 8.94e-25

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 90.97  E-value: 8.94e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYQIELFSFPNPPERKSFPEATGLRHLAFAVTN 84
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVEETDAGEEGGLRSAFFLAGGRVLELLLNETPPPAAAGFGGHHIAFIAFSVDD 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1005575881  85 IEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLEL 125
Cdd:pfam00903  81 VDAAYDRLKAAGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
CatE COG2514
Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
3-126 8.24e-21

Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442004 [Multi-domain]  Cd Length: 141  Bit Score: 81.54  E-value: 8.24e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   3 ISRVHHVAIICSNYERSKNFYTIILGFKEInevyRKERDSYKLdLCVGEEYQIELFSFPNPPERksfPEATGLRHLAFAV 82
Cdd:COG2514     1 ITRLGHVTLRVRDLERSAAFYTDVLGLEVV----EREGGRVYL-RADGGEHLLVLEEAPGAPPR---PGAAGLDHVAFRV 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1005575881  83 TNIEE---AVKHLNQCGVKTEPIRidEITGKKFVFFQDPDGLPLELY 126
Cdd:COG2514    73 PSRADldaALARLAAAGVPVEGAV--DHGVGESLYFRDPDGNLIELY 117
VOC_like cd07245
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 6-125 6.26e-19

uncharacterized subfamily of 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319909 [Multi-domain]  Cd Length: 117  Bit Score: 75.82  E-value: 6.26e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   6 VHHVAIICSNYERSKNFYTIILGFKEInevyrKERDSYKLDLC---VGEEYQIELfSFPNPPERKSFPEATG-LRHLAFA 81
Cdd:cd07245     1 LDHVALACPDLERARRFYTDVLGLEEV-----PRPPFLKFGGAwlyLGGGQQIHL-VVEQNPSELPRPEHPGrDRHPSFS 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1005575881  82 VTNIEEAVKHLNQCGVKTEPiRIDEITGKKFVFFQDPDGLPLEL 125
Cdd:cd07245    75 VPDLDALKQRLKEAGIPYTE-STSPGGGVTQLFFRDPDGNRLEF 117
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 8-125 6.77e-17

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: 70.63  E-value: 6.77e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKeinEVYRKERDSYKLDLCvGEEYQIELFSFPNPPErksfPEATGLRHLAFAVTNIEE 87
Cdd:cd06587     1 HVALRVPDLDASVAFYEEVLGFE---VVSRNEGGGFAFLRL-GPGLRLALLEGPEPER----PGGGGLFHLAFEVDDVDE 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1005575881  88 AVKHLNQCGVKTEPIRIDEIT--GKKFVFFQDPDGLPLEL 125
Cdd:cd06587    73 VDERLREAGAEGELVAPPVDDpwGGRSFYFRDPDGNLIEF 112
VOC_ShValD_like cd16361
vicinal oxygen chelate (VOC) family protein similar to Streptomyces hygroscopicus ValD protein; ...
 5-128 1.37e-13

vicinal oxygen chelate (VOC) family protein similar to Streptomyces hygroscopicus ValD protein; This subfamily of vicinal oxygen chelate (VOC) family protein includes Streptomyces hygroscopicus ValD protein and similar proteins. ValD protein functions in validamycin biosynthetic pathway. 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319968  Cd Length: 150  Bit Score: 63.12  E-value: 1.37e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEInevYR----KERDSYKLDLC-----------------VGEEYQIELFSFPNP 63
Cdd:cd16361     1 GVNHVGITVPDLDAAVEFYTDVLGAEVV---YRstplAEGDRGGGEMRaagfvpgfarariamlrLGPGPGIELFEYKGP 77

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1005575881  64 PERKSFPEA--TGLRHLAFAVTNIEEAVKHL--NQCGVKTEPIRI---DEITGKKFVFFQDPDGLPLELYEV 128
Cdd:cd16361    78 EQRAPVPRNsdVGIFHFALQVDDVEAAAERLaaAGGKVLMGPREIpdgGPGKGNRMVYLRDPWGTLIELVSH 149
VOC COG3324
Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function ...
 5-127 9.55e-11

Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function prediction only];


Pssm-ID: 442553 [Multi-domain]  Cd Length: 119  Bit Score: 55.03  E-value: 9.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFkEINEVYRKERDSYKLDLCVGEEyqIELFSFPNPPERKSFpeatglrHLAFAVTN 84
Cdd:COG3324     4 TIVWVELPVDDLERAKAFYEEVFGW-TFEDDAGPGGDYAEFDTDGGQV--GGLMPGAEEPGGPGW-------LLYFAVDD 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1005575881  85 IEEAVKHLNQCGVK--TEPIRIDEItGkKFVFFQDPDGLPLELYE 127
Cdd:COG3324    74 LDAAVARVEAAGGTvlRPPTDIPPW-G-RFAVFRDPEGNRFGLWQ 116
Glyoxalase_4 pfam13669
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
7-98 8.32e-10

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 463951 [Multi-domain]  Cd Length: 109  Bit Score: 52.28  E-value: 8.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   7 HHVAIICSNYERSKNFYTIILGFKEInEVYRKERDSYKLDLCV--GEEYQIELFSfpnPPERKSFPEA--TGLRHLAFAV 82
Cdd:pfam13669   1 HHVGIAVPDLDRALALWGALLGLGPE-GDYRSEPQNVDLAFALlgDGPVEVELIQ---PLDGDSPLARhgPGLHHLAYWV 76

                          90
                  ....*....|....*.
gi 1005575881  83 TNIEEAVKHLNQCGVK 98
Cdd:pfam13669  77 DDLDAAVARLLDQGYR 92
GLOD5 cd07253
Human glyoxalase domain-containing protein 5 and similar proteins; Uncharacterized subfamily ...
 3-125 9.41e-10

Human glyoxalase domain-containing protein 5 and similar proteins; Uncharacterized subfamily of VOC family contains human glyoxalase domain-containing protein 5 and similar proteins. 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319916 [Multi-domain]  Cd Length: 123  Bit Score: 52.23  E-value: 9.41e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   3 ISRVHHVAIICSNYERSKNFYTIILGFKEINevYRKERDSykldLCVGEEYqIELFSFPNPPERKSFPEATGLRHLAFAV 82
Cdd:cd07253     1 IKRLDHLVLTVKDIERTIDFYTKVLGMTVVT--FKEGRKA----LRFGNQK-INLHQKGKEFEPKASAPTPGSADLCFIT 73

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1005575881  83 -TNIEEAVKHLNQCGVKTE--PIR----IDEITGkkfVFFQDPDGLPLEL 125
Cdd:cd07253    74 eTPIDEVLEHLEACGVTIEegPVKrtgaLGPILS---IYFRDPDGNLIEL 120
MMCE cd07249
Methylmalonyl-CoA epimerase (MMCE); MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) ...
 6-127 3.30e-09

Methylmalonyl-CoA epimerase (MMCE); MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) interconverts (2R)-methylmalonyl-CoA and (2S)-methylmalonyl-CoA. MMCE has been found in bacteria, archaea, and in animals. In eukaryotes, MMCE is an essential enzyme in a pathway that converts propionyl-CoA to succinyl-CoA, and is important in the breakdown of odd-chain length fatty acids, branched-chain amino acids, and other metabolites. In bacteria, MMCE participates in the reverse pathway for propionate fermentation, glyoxylate regeneration, and the biosynthesis of polyketide antibiotics. MMCE is closely related to glyoxalase I and type I extradiol dioxygenases.


Pssm-ID: 319912 [Multi-domain]  Cd Length: 127  Bit Score: 51.04  E-value: 3.30e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   6 VHHVAIICSNYERSKNFYTIILGFKEineVYRKERDSYKLDLCVGE--EYQIEL---FSfPNPPERKSFPE-ATGLRHLA 79
Cdd:cd07249     1 LDHIGIAVPDLDEALKFYEDVLGVKV---SEPEELEEQGVRVAFLElgNTQIELlepLG-EDSPIAKFLDKkGGGLHHIA 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1005575881  80 FAVTNIEEAVKHLNQCGVKT-EPIRIDEITGKKFVFFQDPD--GLPLELYE 127
Cdd:cd07249    77 FEVDDIDAAVEELKAQGVRLlSEGPRIGAHGKRVAFLHPKDtgGVLIELVE 127
metmalonyl_epim TIGR03081
methylmalonyl-CoA epimerase; Members of this protein family are the enzyme methylmalonyl-CoA ...
 5-127 1.36e-08

methylmalonyl-CoA epimerase; Members of this protein family are the enzyme methylmalonyl-CoA epimerase (EC 5.1.99.1), also called methylmalonyl-CoA racemase. This enzyme converts (2R)-methylmalonyl-CoA to (2S)-methylmalonyl-CoA, which is then a substrate for methylmalonyl-CoA mutase (TIGR00642). It is known in bacteria, archaea, and as a mitochondrial protein in animals. It is closely related to lactoylglutathione lyase (TIGR00068), which is also called glyoxylase I, and is also a homodimer.


Pssm-ID: 213772 [Multi-domain]  Cd Length: 128  Bit Score: 49.63  E-value: 1.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYqIELFsfpNPPERKS----FPEAT--GLRHL 78
Cdd:TIGR03081   1 RIDHVGIAVPDLEEAAKFYEDVLGAQVSEIEELPEQGVKVVFIALGNTK-VELL---EPLGEDSpiakFLEKNggGIHHI 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1005575881  79 AFAVTNIEEAVKHLNQCGVKtepiRIDEIT-----GKKFVFF--QDPDGLPLELYE 127
Cdd:TIGR03081  77 AIEVDDIEAALETLKEKGVR----LIDEEPrigahGKPVAFLhpKSTGGVLIELEQ 128
VOC_like cd07264
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 8-127 4.36e-08

uncharacterized subfamily of 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319925 [Multi-domain]  Cd Length: 118  Bit Score: 48.10  E-value: 4.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKEinevyrkerdSYKLDLCVGEEYQ-----IELFSFPNPPERKSFPEATGLRHLAFAV 82
Cdd:cd07264     3 YIVLYVDDFAASLRFYRDVLGLPP----------RFLHEEGEYAEFDtgetkLALFSRKEMARSGGPDRRGSAFELGFEV 72

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1005575881  83 TNIEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELYE 127
Cdd:cd07264    73 DDVEATVEELVERGAEFVREPANKPWGQTVAYVRDPDGNLIEICE 117
ED_TypeI_classII_N cd16360
N-terminal domain of type I, class II extradiol dioxygenases; This family contains the ...
 8-126 5.60e-07

N-terminal domain of type I, class II extradiol dioxygenases; This family contains the N-terminal non-catalytic domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon, whereas intradiol enzymes cleave the aromatic ring between two hydroxyl groups. Extradiol dioxygenases are classified into type I and type II enzymes. Type I extradiol dioxygenases include class I and class II enzymes. These two classes of enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. The extradiol dioxygenases represented in this family are type I, class II enzymes, and are composed of the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. A catalytically essential metal, Fe(II) or Mn(II), presents in all the enzymes in this family.


Pssm-ID: 319967  Cd Length: 111  Bit Score: 45.00  E-value: 5.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKEI----NEVYRKERDSYKLDLCVGEEyqielfsfpnpperksfPEAtGLRHLAFAVT 83
Cdd:cd16360     1 YAELGVPDLEKALEFYTDVLGLQVAkrdgNSVYLRGYEDEHHSLVLYEA-----------------PEA-GLKHFAFEVA 62

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1005575881  84 N---IEEAVKHLNQCGVKTEPIRIDEITG-KKFVFFQDPDGLPLELY 126
Cdd:cd16360    63 SeedLERAAASLTALGCDVTWGPDGEVPGgGKGFRFQDPSGHLLELF 109
GLOD4_C cd16357
C-terminal domain of human glyoxalase domain-containing protein 4 and similar proteins; ...
 8-120 5.65e-07

C-terminal domain of human glyoxalase domain-containing protein 4 and similar proteins; Uncharacterized subfamily of the vicinal oxygen chelate (VOC) superfamily contains human glyoxalase domain-containing protein 4 and similar proteins. VOC 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319964  Cd Length: 114  Bit Score: 44.85  E-value: 5.65e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKEInevyrkERDSYKLDLCVGEEYQ-IELFSFPNPPERksfpeATGLRHLAFAV---- 82
Cdd:cd16357     1 KVSLAVSDLEKSIDYWSDLLGMKVF------EKSEKSALLGYGEDQAkLELVDIPEPVDH-----GTAFGRIAFSCpade 69

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1005575881  83 -TNIEEAVKHLNQcGVKTEPIRIDeiT-GKK---FVFFQDPDG 120
Cdd:cd16357    70 lPPIEEKVKAAGQ-TILTPLVSLD--TpGKAtvqVVILADPDG 109
VOC_BsCatE_like_N cd07255
N-terminal of Bacillus subtilis CatE like protein; Uncharacterized subfamily of VOC ...
 5-126 1.27e-06

N-terminal of Bacillus subtilis CatE like protein; Uncharacterized subfamily of VOC superfamily contains Bacillus subtilis CatE and similar proteins. CatE is proposed to function as Catechol-2,3-dioxygenase. VOC 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319918  Cd Length: 124  Bit Score: 44.22  E-value: 1.27e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGFKEInevyrkERDSYKLDLCV-GEEYQIELFSFPNPPERKsfPEATGLRHLAFAVT 83
Cdd:cd07255     2 RIGRVTLKVADLERQSAFYQNVIGLSVL------KQNASRAYLGVdGKQVLLVLEAIPDAVLAP--RSTTGLYHFAILLP 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1005575881  84 NIEE---AVKHLNQCGVKTEPirIDEITGKKFvFFQDPDGLPLELY 126
Cdd:cd07255    74 DRKAlgrALAHLAEHGPLIGA--ADHGVSEAI-YLSDPEGNGIEIY 116
VOC_like cd08353
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 52-92 1.38e-06

uncharacterized subfamily of 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319941  Cd Length: 142  Bit Score: 44.49  E-value: 1.38e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1005575881  52 EYQIELFSFPNPP----ERKSFPEATGLRHLAFAVTNIEEAVKHL 92
Cdd:cd08353    61 HGRLELSKFLTPAaipgHRPAPANALGLRHVAFAVDDIDAVVARL 105
BphC-JF8_N_like cd09013
N-terminal, non-catalytic, domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from ...
 3-126 1.73e-06

N-terminal, non-catalytic, domain of BphC_JF8, (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Bacillus sp. JF8, and similar proteins; 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, a key step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). BphC belongs to the type I extradiol dioxygenase family, which requires a metal ion in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. This subfamily of BphC is represented by the enzyme purified from the thermophilic biphenyl and naphthalene degrader, Bacillus sp. JF8. The members in this family of BphC enzymes may use either Mn(II) or Fe(II) as cofactors. The enzyme purified from Bacillus sp. JF8 is Mn(II)-dependent, however, the enzyme from Rhodococcus jostii RHAI has Fe(II) bound to it. BphC_JF8 is thermostable and its optimum activity is at 85 degrees C. The enzymes in this family have an internal duplication. This family represents the N-terminal repeat.


Pssm-ID: 319955  Cd Length: 121  Bit Score: 43.88  E-value: 1.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   3 ISRVHHVAIICSNYERSKNFYTIILGFKEI----NEVYRKERDSYkldlcvgEEYQIELFSFPNPperksfpeatGLRHL 78
Cdd:cd09013     4 LAQLAHVELLTPKPEESLWFFTDVLGLEEThregQSVYLRAWGDW-------EHHTLKLTESPEA----------GLGHI 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1005575881  79 AFAVTN---IEEAVKHLNQCGVKTEPIRIDEITGKKFVfFQDPDGLPLELY 126
Cdd:cd09013    67 AWRASSpeaLERRVAALEASGVGIGWIDGDLGQGPAYR-FQSPDGHPMEIY 116
HPCD_N_class_II cd07266
N-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD); This subfamily ...
 2-126 2.07e-06

N-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD); This subfamily contains the N-terminal, non-catalytic, domain of HPCD. HPCD catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. The aromatic ring of 4-hydroxyphenylacetate is opened by this dioxygenase to yield the 3,4-diol product, 2-hydroxy-5-carboxymethylmuconate semialdehyde. HPCD is a homotetramer and each monomer contains two structurally homologous barrel-shaped domains at the N- and C-terminus. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. Most extradiol dioxygenases contain Fe(II) in their active site, but HPCD can be activated by either Mn(II) or Fe(II). These enzymes belong to the type I class II family of extradiol dioxygenases. The class III 3,4-dihydroxyphenylacetate 2,3-dioxygenases belong to a different superfamily.


Pssm-ID: 319927  Cd Length: 118  Bit Score: 43.55  E-value: 2.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   2 NISRVHHVAIICSNYERSKNFYTIILGFKEINEvyrkerDSYKLDLCVGEEYQ---IELFSFPNPperksfpeatGLRHL 78
Cdd:cd07266     1 DIIRLAHAELVVTDLAASREFYVDTLGLHVTDE------DDNAIYLRGVEEFIhhtLVLRKAPEA----------AVGHL 64

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1005575881  79 AFAVTN---IEEAVKHLNQCGVKTEpiRIDEITGKKFVFFQDPDGLPLELY 126
Cdd:cd07266    65 GFRVRDeadLDKAAAFYKELGLPTE--WREEPGQGRTLRVEDPFGFPIEFY 113
VOC_BsYyaH cd07241
vicinal oxygen chelate (VOC) family protein similar to Bacillus subtilis YyaH; The vicinal ...
 5-94 2.16e-06

vicinal oxygen chelate (VOC) family protein similar to Bacillus subtilis YyaH; 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319905  Cd Length: 125  Bit Score: 43.55  E-value: 2.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   5 RVHHVAIICSNYERSKNFYTIILGfKEINEVYRKERDSYK-LDLCVGEEYQIELFSFPNPPERKSFPEATGLRHLAFAVT 83
Cdd:cd07241     1 KIEHVALWTNDLERMKDFYVKYFG-AESNDIYHNKKKGFRsYFLTFDSGARLELMSRPDVTDPDKEVERTGLAHIAFSVG 79

                          90
                  ....*....|.
gi 1005575881  84 NiEEAVKHLNQ 94
Cdd:cd07241    80 S-KEAVDELTE 89
VOC_like cd07263
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 8-120 3.17e-06

uncharacterized subfamily of 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping


Pssm-ID: 319924 [Multi-domain]  Cd Length: 120  Bit Score: 43.05  E-value: 3.17e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKEINEVYrkerdsykldlcVGEEYQIELFSfPNPPE------RKSFPEAT-------- 73
Cdd:cd07263     1 QVMLYVDDQDKALDFYVEKLGFEVVEDVP------------MGGMRWVTVAP-PGSPGtslllePKAHPAQMpqspeaag 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1005575881  74 GLRHLAFAVTNIEEAVKHLNQCGVKTEPIRIDEITGKKFVfFQDPDG 120
Cdd:cd07263    68 GTPGILLATDDIDATYERLTAAGVTFVQEPTQMGGGRVAN-FRDPDG 113
BphC5-RrK37_N_like cd08362
N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from ...
 3-125 5.45e-06

N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Rhodococcus rhodochrous K37, and similar proteins; 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting from an ancient gene duplication. BphC belongs to the type I extradiol dioxygenase family, which requires a metal in the active site for its catalytic activity. Polychlorinated biphenyl degrading bacteria demonstrate multiplicity of BphCs. Bacterium Rhodococcus rhodochrous K37 has eight genes encoding BphC enzymes. This family includes the N-terminal domain of BphC5-RrK37. The crystal structure of the protein from Novosphingobium aromaticivorans has a Mn(II)in the active site, although most proteins of type I extradiol dioxygenases are activated by Fe(II).


Pssm-ID: 319950 [Multi-domain]  Cd Length: 120  Bit Score: 42.62  E-value: 5.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   3 ISRVHHVAIICSNYERSKNFYTIILGFKEINEvyrkERDSYKLDLCVGEEYQIELfsfpnppeRKSfpEATGLRHLAFAV 82
Cdd:cd08362     1 VTHLRYVALGVPDLAAEREFYTEVWGLEEVAE----DDDVVYLRAEGSEHHVLRL--------RQS--DENRLDLIAFAA 66

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1005575881  83 ---TNIEEAVKHLNQCGVK--TEPIRIDEIT-GKKFVFFqDPDGLPLEL 125
Cdd:cd08362    67 atrADVDALAARLAAAGVRilSEPGPLDDPGgGYGFRFF-DPDGRTIEV 114
GlxI_Ni cd16358
Glyoxalase I that uses Ni(++) as cofactor; This family includes Escherichia coil and other ...
 8-125 8.92e-06

Glyoxalase I that uses Ni(++) as cofactor; This family includes Escherichia coil and other prokaryotic glyoxalase I that uses nickel as cofactor. Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes into the corresponding alpha-hydroxyacids and involves 2 enzymes, glyoxalase I and II. Glyoxalase I catalyses an intramolecular redox reaction of the hemithioacetal (formed from methylglyoxal and glutathione) to form the thioester, S-D-lactoylglutathione. This reaction involves the transfer of two hydrogen atoms from C1 to C2 of the methylglyoxal, and proceeds via an ene-diol intermediate. Glyoxalase I has a requirement for bound metal ions for catalysis. Eukaryotic glyoxalase I prefers the divalent cation zinc as cofactor, whereas Escherichia coil and other prokaryotic glyoxalase I uses nickel. However, eukaryotic Trypanosomatid parasites also use nickel as a cofactor, which could possibly be explained by acquiring their GLOI gene by horizontal gene transfer. Human glyoxalase I is a two-domain enzyme and it has the structure of a domain-swapped dimer with two active sites located at the dimer interface. In yeast, in various plants, insects and Plasmodia, glyoxalase I is four-domain, possibly the result of a further gene duplication and an additional gene fusing event.


Pssm-ID: 319965 [Multi-domain]  Cd Length: 122  Bit Score: 42.00  E-value: 8.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKEINevyRKERDSYKLDLC-VG-----EEYQIEL-FSFpnppERKSFPEATGLRHLAF 80
Cdd:cd16358     3 HTMLRVGDLDRSIKFYTEVLGMKLLR---KRDYPEGKYTLAfVGygdedENTVLELtYNW----GVDKYDLGTAYGHIAI 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1005575881  81 AVTNIEEAVKHLNQCGVKT--EPIRIDEITGkKFVFFQDPDGLPLEL 125
Cdd:cd16358    76 GVEDVYETCERIRKKGGKVtrEPGPMKGGTT-VIAFVEDPDGYKIEL 121
Fosfomycin_RP cd08345
Fosfomycin resistant protein; This family contains three types of fosfomycin resistant protein. ...
 8-126 2.07e-05

Fosfomycin resistant protein; This family contains three types of fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. The three types of fosfomycin resistance proteins, employ different mechanisms to render fosfomycin [(1R,2S)-epoxypropylphosphonic acid] inactive. FosB catalyzes the addition of L-cysteine to the epoxide ring of fosfomycin. FosX catalyzes the addition of a water molecule to the C1 position of the antibiotic with inversion of configuration at C1. FosA catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive. Catalytic activities of both FosX and FosA are Mn(II)-dependent, but FosB is activated by Mg(II). Fosfomycin resistant proteins are evolutionarily related to glyoxalase I and type I extradiol dioxygenases.


Pssm-ID: 319933  Cd Length: 118  Bit Score: 41.00  E-value: 2.07e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKeinEVYRKERDSYKLD-----------LCVGEEyqielfsfPNPPERKsfpeatgLR 76
Cdd:cd08345     1 HITLIVRDLEKSTAFLQDIFGAR---EVYSSGDKTFSLSkekffllgglwIALMEG--------ESLQERS-------YT 62

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1005575881  77 HLAFAVTNIEEAV--KHLNQCGVKTEPIR-IDEITGKKFvFFQDPDGLPLELY 126
Cdd:cd08345    63 HIAFQIQSEDFDRyaERLGALGVEMRPPRpRVEGEGRSI-YFYDPDNHLFELH 114
ED_TypeI_classII_C cd08343
C-terminal domain of type I, class II extradiol dioxygenases, catalytic domain; This family ...
 8-126 2.02e-04

C-terminal domain of type I, class II extradiol dioxygenases, catalytic domain; This family contains the C-terminal, catalytic domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon, whereas intradiol enzymes cleave the aromatic ring between two hydroxyl groups. Extradiol dioxygenases are classified into type I and type II enzymes. Type I extradiol dioxygenases include class I and class II enzymes. These two classes of enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. The extradiol dioxygenases represented in this family are type I, class II enzymes, and are composed of the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. A catalytically essential metal, Fe(II) or Mn(II), presents in all the enzymes in this family.


Pssm-ID: 319931  Cd Length: 132  Bit Score: 38.45  E-value: 2.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   8 HVAIICSNYERSKNFYTIILGFKEINEVYRKERDSYKLDLCVGEEYQIELFSFPNPPerksfpeaTGLRHLAFAVTNIEE 87
Cdd:cd08343     2 HVVLCSPDVEASRDFYTDVLGFRVSDRIVDPGVDGGAFLHCDRGTDHHTVALAGGPH--------PGLHHVAFEVHDLDD 73

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1005575881  88 ---AVKHLNQCGVKTE--PIRiDEITGKKFVFFQDPDGLPLELY 126
Cdd:cd08343    74 vgrGHDRLREKGYKIEwgPGR-HGLGSQVFDYWFDPSGNRVEYY 116
HppD COG3185
4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and ...
 1-98 2.36e-04

4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and metabolism, General function prediction only];


Pssm-ID: 442418 [Multi-domain]  Cd Length: 333  Bit Score: 39.10  E-value: 2.36e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   1 MNISRVHHVAIICS--NYERSKNFYTIILGFKEINEV-----YRKERdSYKLDLCVGEeYQIELfsfpN-PPERKS---- 68
Cdd:COG3185   142 AGLTRIDHIGIAVPrgDLDEWVLFYEDVLGFEEIREEdiedpYQGVR-SAVLQSPDGK-VRIPL----NePTSPDSqiae 215

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1005575881  69 FPEAT---GLRHLAFAVTNIEEAVKHLNQCGVK 98
Cdd:COG3185   216 FLEKYrgeGIQHIAFATDDIEATVAALRARGVR 248
GlxI_Zn cd07233
Glyoxalase I that uses Zn(++) as cofactor; This family includes eukaryotic glyoxalase I that ...
 17-125 2.61e-04

Glyoxalase I that uses Zn(++) as cofactor; This family includes eukaryotic glyoxalase I that prefers the divalent cation zinc as cofactor. Glyoxalase I (also known as lactoylglutathione lyase; EC 4.4.1.5) is part of the glyoxalase system, a two-step system for detoxifying methylglyoxal, a side product of glycolysis. This system is responsible for the conversion of reactive, acyclic alpha-oxoaldehydes into the corresponding alpha-hydroxyacids and involves 2 enzymes, glyoxalase I and II. Glyoxalase I catalyses an intramolecular redox reaction of the hemithioacetal (formed from methylglyoxal and glutathione) to form the thioester, S-D-lactoylglutathione. This reaction involves the transfer of two hydrogen atoms from C1 to C2 of the methylglyoxal, and proceeds via an ene-diol intermediate. Glyoxalase I has a requirement for bound metal ions for catalysis. Eukaryotic glyoxalase I prefers the divalent cation zinc as cofactor, whereas Escherichia coil and other prokaryotic glyoxalase I uses nickel. However, eukaryotic Trypanosomatid parasites also use nickel as a cofactor, which could possibly be explained by acquiring their GLOI gene by horizontal gene transfer. Human glyoxalase I is a two-domain enzyme and it has the structure of a domain-swapped dimer with two active sites located at the dimer interface. In yeast, in various plants, insects and Plasmodia, glyoxalase I is four-domain, possibly the result of a further gene duplication and an additional gene fusing event.


Pssm-ID: 319900 [Multi-domain]  Cd Length: 142  Bit Score: 38.46  E-value: 2.61e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881  17 ERSKNFYTIILGFKEINEvYRKERDSYKL------DLCVGEEYQIELFSFPNPP----------ERKSFP-------EAT 73
Cdd:cd07233    12 KKSLKFYTEVLGMKLLRK-KDFPEMKFSLyflgyeDPKDIPKDPRTAWVFSREGtlelthnwgtENDEDPvyhngnsDPR 90

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1005575881  74 GLRHLAFAVTNIEEAVKHLNQCGVKTEPiRIDEITGKKFVFFQDPDGLPLEL 125
Cdd:cd07233    91 GFGHIGIAVDDVYAACERFEELGVKFKK-KPDDGKMKGIAFIKDPDGYWIEI 141
VOC_BsYqjT cd07242
vicinal oxygen chelate (VOC) family protein similar to Bacillus subtilis YqjT; The vicinal ...
 6-125 9.51e-04

vicinal oxygen chelate (VOC) family protein similar to Bacillus subtilis YqjT; 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 domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. 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). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319906  Cd Length: 126  Bit Score: 36.70  E-value: 9.51e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   6 VHHVAIICSNYERSKNFYTIIL--GFKEINEVYR----KERDSYKLDLCVGEEYQIELFSFPNPperksfpeatGLRHLA 79
Cdd:cd07242     2 VSHVELAVSDLHRSFKWFEWILglGWKEYDTWSFgpswKLSGGSLLVVQQTDEFATPEFDRARV----------GLNHLA 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1005575881  80 FAV---TNIEEAVKHLNQCG---VKTEPIRIDEITGKKFVFFQDPDGLPLEL 125
Cdd:cd07242    72 FHAesrEAVDELTEKLAKIGgvrTYGDRHPFAGGPPHYAAFCEDPDGIKLEL 123
BphC2-C3-RGP6_C_like cd08348
The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases; This subfamily contains Rhodococcus ...
 16-125 1.10e-03

The single-domain 2,3-dihydroxybiphenyl 1,2-dioxygenases; This subfamily contains Rhodococcus globerulus P6 BphC2-RGP6 and BphC3-RGP6, and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, yielding 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. This is the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Most type I extradiol dioxygenases are activated by Fe(II). Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases, which form hexamers. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, its two domains do not belong to this subfamily.


Pssm-ID: 319936  Cd Length: 137  Bit Score: 36.34  E-value: 1.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881  16 YERSKNFYTIILGfkeINEVYRKERDSYkldLCVGEE-YQIELFSFPN---PPERKsfPEATGLRHLAFAVTNIEEAVKh 91
Cdd:cd08348    14 FEAMVQWYLDILG---ARIVARNAKGCF---LSFDEEhHRIAIFGAPGgaqPPDKR--PTRVGLAHIAFTYASLDDLAR- 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1005575881  92 lNQCGVKTEPIRIDEI------TGkkfVFFQDPDGLPLEL 125
Cdd:cd08348    85 -NYAQLKERGIKPVWPvnhgvtTS---IYYRDPDGNMLEM 120
PRK10291 PRK10291
glyoxalase I; Provisional
 15-127 1.36e-03

glyoxalase I; Provisional


Pssm-ID: 182358  Cd Length: 129  Bit Score: 36.15  E-value: 1.36e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881  15 NYERSKNFYTIILGFKEINEvyrKERDSYKLDLCV---GEEYQIELFSFPNPPERKSFPEATGLRHLAFAVTNIEEAVKH 91
Cdd:PRK10291    6 DLQRSIDFYTNVLGMKLLRT---SENPEYKYSLAFvgyGPETEEAVIELTYNWGVDKYELGTAYGHIALSVDNAAEACEK 82

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1005575881  92 LNQCG--VKTE--PIRIDEITgkkFVFFQDPDGLPLELYE 127
Cdd:PRK10291   83 IRQNGgnVTREagPVKGGTTV---IAFVEDPDGYKIELIE 119
PRK04101 PRK04101
metallothiol transferase FosB;
2-126 2.65e-03

metallothiol transferase FosB;


Pssm-ID: 179740  Cd Length: 139  Bit Score: 35.31  E-value: 2.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1005575881   2 NISRVHHVAIICSNYERSKNFYTIILGFKEInevYRKERDSYkLDLC-----VGEEYQIelfsfPNPPERKSFPeatglr 76
Cdd:PRK04101    1 MLKGINHICFSVSNLEKSIEFYEKVLGAKLL---VKGRKTAY-FDLNglwiaLNEEKDI-----PRNEIHQSYT------ 65

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1005575881  77 HLAFAVTN--IEEAVKHLNQCGVKTEPIRIDEITGKKFVFFQDPDGLPLELY 126
Cdd:PRK04101   66 HIAFSIEEedFDHWYQRLKENDVNILPGRERDERDKKSIYFTDPDGHKFEFH 117
 
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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