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Conserved domains on  [gi|530368214|ref|XP_005264670|]
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methylmalonyl-CoA epimerase, mitochondrial isoform X2 [Homo sapiens]

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VOC super family cl14632
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 47-121 1.24e-32

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.


The actual alignment was detected with superfamily member TIGR03081:

Pssm-ID: 472697 [Multi-domain]  Cd Length: 128  Bit Score: 110.88  E-value: 1.24e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214   47 RLNHVAIAVPDLEKAAAFYKNILGAQ-----------------------------------------------------V 73
Cdd:TIGR03081   1 RIDHVGIAVPDLEEAAKFYEDVLGAQvseieelpeqgvkvvfialgntkvelleplgedspiakflekngggihhiaieV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 530368214   74 DNINAAVMDLKKKKIRSLSEEVKIGAHGKPVIFLHPKDCGGVLVELEQ 121
Cdd:TIGR03081  81 DDIEAALETLKEKGVRLIDEEPRIGAHGKPVAFLHPKSTGGVLIELEQ 128
 
Name Accession Description Interval E-value
metmalonyl_epim TIGR03081
methylmalonyl-CoA epimerase; Members of this protein family are the enzyme methylmalonyl-CoA ...
 47-121 1.24e-32

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: 110.88  E-value: 1.24e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214   47 RLNHVAIAVPDLEKAAAFYKNILGAQ-----------------------------------------------------V 73
Cdd:TIGR03081   1 RIDHVGIAVPDLEEAAKFYEDVLGAQvseieelpeqgvkvvfialgntkvelleplgedspiakflekngggihhiaieV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 530368214   74 DNINAAVMDLKKKKIRSLSEEVKIGAHGKPVIFLHPKDCGGVLVELEQ 121
Cdd:TIGR03081  81 DDIEAALETLKEKGVRLIDEEPRIGAHGKPVAFLHPKSTGGVLIELEQ 128
MMCE cd07249
Methylmalonyl-CoA epimerase (MMCE); MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) ...
 48-121 4.74e-28

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: 99.19  E-value: 4.74e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214  48 LNHVAIAVPDLEKAAAFYKNILGAQ-----------------------------------------------------VD 74
Cdd:cd07249    1 LDHIGIAVPDLDEALKFYEDVLGVKvsepeeleeqgvrvaflelgntqielleplgedspiakfldkkggglhhiafeVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 530368214  75 NINAAVMDLKKKKIRSLSEEVKIGAHGKPVIFLHPKDCGGVLVELEQ 121
Cdd:cd07249   81 DIDAAVEELKAQGVRLLSEGPRIGAHGKRVAFLHPKDTGGVLIELVE 127
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 47-119 1.02e-09

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: 52.30  E-value: 1.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214  47 RLNHVAIAVPDLEKAAAFYKNILGAQ------------------------------------------------VDNINA 78
Cdd:COG0346    2 GLHHVTLRVSDLEASLAFYTDVLGLElvkrtdfgdggfghaflrlgdgtelelfeapgaapapgggglhhlafrVDDLDA 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 530368214  79 AVMDLKKKKIRsLSEEVKIGAHGKPVIFLhpKDCGGVLVEL 119
Cdd:COG0346   82 AYARLRAAGVE-IEGEPRDRAYGYRSAYF--RDPDGNLIEL 119
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
47-73 7.23e-07

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 44.75  E-value: 7.23e-07
                          10        20
                  ....*....|....*....|....*..
gi 530368214   47 RLNHVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKL 27
PRK04101 PRK04101
metallothiol transferase FosB;
48-72 5.63e-03

metallothiol transferase FosB;


Pssm-ID: 179740  Cd Length: 139  Bit Score: 34.54  E-value: 5.63e-03
                         10        20
                 ....*....|....*....|....*
gi 530368214  48 LNHVAIAVPDLEKAAAFYKNILGAQ 72
Cdd:PRK04101   5 INHICFSVSNLEKSIEFYEKVLGAK 29
 
Name Accession Description Interval E-value
metmalonyl_epim TIGR03081
methylmalonyl-CoA epimerase; Members of this protein family are the enzyme methylmalonyl-CoA ...
 47-121 1.24e-32

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: 110.88  E-value: 1.24e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214   47 RLNHVAIAVPDLEKAAAFYKNILGAQ-----------------------------------------------------V 73
Cdd:TIGR03081   1 RIDHVGIAVPDLEEAAKFYEDVLGAQvseieelpeqgvkvvfialgntkvelleplgedspiakflekngggihhiaieV 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 530368214   74 DNINAAVMDLKKKKIRSLSEEVKIGAHGKPVIFLHPKDCGGVLVELEQ 121
Cdd:TIGR03081  81 DDIEAALETLKEKGVRLIDEEPRIGAHGKPVAFLHPKSTGGVLIELEQ 128
MMCE cd07249
Methylmalonyl-CoA epimerase (MMCE); MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) ...
 48-121 4.74e-28

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: 99.19  E-value: 4.74e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214  48 LNHVAIAVPDLEKAAAFYKNILGAQ-----------------------------------------------------VD 74
Cdd:cd07249    1 LDHIGIAVPDLDEALKFYEDVLGVKvsepeeleeqgvrvaflelgntqielleplgedspiakfldkkggglhhiafeVD 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 530368214  75 NINAAVMDLKKKKIRSLSEEVKIGAHGKPVIFLHPKDCGGVLVELEQ 121
Cdd:cd07249   81 DIDAAVEELKAQGVRLLSEGPRIGAHGKRVAFLHPKDTGGVLIELVE 127
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 47-119 1.02e-09

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: 52.30  E-value: 1.02e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214  47 RLNHVAIAVPDLEKAAAFYKNILGAQ------------------------------------------------VDNINA 78
Cdd:COG0346    2 GLHHVTLRVSDLEASLAFYTDVLGLElvkrtdfgdggfghaflrlgdgtelelfeapgaapapgggglhhlafrVDDLDA 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 530368214  79 AVMDLKKKKIRsLSEEVKIGAHGKPVIFLhpKDCGGVLVEL 119
Cdd:COG0346   82 AYARLRAAGVE-IEGEPRDRAYGYRSAYF--RDPDGNLIEL 119
HppD COG3185
4-hydroxyphenylpyruvate dioxygenase and related hemolysins [Amino acid transport and ...
 45-119 4.01e-09

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: 52.58  E-value: 4.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214  45 LGRLNHVAIAVP--DLEKAAAFYKNILGAQ-------------------------------------------------- 72
Cdd:COG3185  144 LTRIDHIGIAVPrgDLDEWVLFYEDVLGFEeireediedpyqgvrsavlqspdgkvriplneptspdsqiaeflekyrge 223

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 530368214  73 --------VDNINAAVMDLKKKKIRSLSE--------EVKIGAHGKPVIFLHPK------DCGGVLVEL 119
Cdd:COG3185  224 giqhiafaTDDIEATVAALRARGVRFLDIpdnyyddlEPRVGAHGEDVAFLHPKgilvdrDTGGVLLQI 292
VOC_like cd07245
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 48-70 5.38e-07

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: 45.00  E-value: 5.38e-07
                         10        20
                 ....*....|....*....|...
gi 530368214  48 LNHVAIAVPDLEKAAAFYKNILG 70
Cdd:cd07245    1 LDHVALACPDLERARRFYTDVLG 23
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
47-73 7.23e-07

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 44.75  E-value: 7.23e-07
                          10        20
                  ....*....|....*....|....*..
gi 530368214   47 RLNHVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKL 27
CatE COG2514
Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
47-73 1.10e-06

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


Pssm-ID: 442004 [Multi-domain]  Cd Length: 141  Bit Score: 44.56  E-value: 1.10e-06
                         10        20
                 ....*....|....*....|....*..
gi 530368214  47 RLNHVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:COG2514    3 RLGHVTLRVRDLERSAAFYTDVLGLEV 29
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 50-73 5.64e-06

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: 42.13  E-value: 5.64e-06
                         10        20
                 ....*....|....*....|....
gi 530368214  50 HVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:cd06587    1 HVALRVPDLDASVAFYEEVLGFEV 24
VOC_ShValD_like cd16361
vicinal oxygen chelate (VOC) family protein similar to Streptomyces hygroscopicus ValD protein; ...
 47-73 1.28e-05

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: 41.93  E-value: 1.28e-05
                         10        20
                 ....*....|....*....|....*..
gi 530368214  47 RLNHVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:cd16361    1 GVNHVGITVPDLDAAVEFYTDVLGAEV 27
Glyoxalase_4 pfam13669
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
49-106 2.81e-05

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 463951 [Multi-domain]  Cd Length: 109  Bit Score: 40.34  E-value: 2.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214   49 NHVAIAVPDLEKAAAFYKNILGAQ---------------------------------------------------VDNIN 77
Cdd:pfam13669   1 HHVGIAVPDLDRALALWGALLGLGpegdyrsepqnvdlafallgdgpveveliqpldgdsplarhgpglhhlaywVDDLD 80

                          90       100
                  ....*....|....*....|....*....
gi 530368214   78 AAVMDLKKKKIRSLSEEVKIGAHGKPVIF 106
Cdd:pfam13669  81 AAVARLLDQGYRVAPKGPRAGAAGRRVAF 109
VOC COG3324
Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function ...
 46-122 4.09e-05

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


Pssm-ID: 442553 [Multi-domain]  Cd Length: 119  Bit Score: 40.00  E-value: 4.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530368214  46 GRLNHVAIAVPDLEKAAAFYKNILGAQVD-----NINAAVMDLKKKKIRSLSEEVKIGAHGKPVIFLHPKDCGGVLVELE 120
Cdd:COG3324    3 GTIVWVELPVDDLERAKAFYEEVFGWTFEddagpGGDYAEFDTDGGQVGGLMPGAEEPGGPGWLLYFAVDDLDAAVARVE 82


                 ..
gi 530368214 121 QA 122
Cdd:COG3324   83 AA 84
FosA cd07244
fosfomycin resistant protein subfamily FosA; This subfamily family contains FosA, a fosfomycin ...
 48-70 1.46e-04

fosfomycin resistant protein subfamily FosA; This subfamily family contains FosA, a fosfomycin resistant protein. FosA is a Mn(II) and K(+)-dependent glutathione transferase. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. FosA, catalyzes the addition of glutathione to the antibiotic fosfomycin, (1R,2S)-epoxypropylphosphonic acid, making it inactive. FosA is a Mn(II) dependent enzyme. It is evolutionarily related to glyoxalase I and type I extradiol dioxygenases.


Pssm-ID: 319908 [Multi-domain]  Cd Length: 121  Bit Score: 38.42  E-value: 1.46e-04
                         10        20
                 ....*....|....*....|...
gi 530368214  48 LNHVAIAVPDLEKAAAFYKNILG 70
Cdd:cd07244    2 INHITLAVSDLERSLAFYVDLLG 24
VOC_Bs_YwkD_like cd08352
vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; ...
 47-73 3.33e-04

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: 37.52  E-value: 3.33e-04
                         10        20
                 ....*....|....*....|....*..
gi 530368214  47 RLNHVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:cd08352    2 KIHHIAIICSDYEKSKDFYVDKLGFEI 28
BphC1-RGP6_C_like cd07237
C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase; This subfamily contains the ...
 38-89 1.06e-03

C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase; This subfamily contains the C-terminal, catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, 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. 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. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, and has Fe(II) at the catalytic site. Its C-terminal repeat is represented in this subfamily. BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases, they belong to a different subfamily of the ED_TypeI_classII_C (C-terminal domain of type I, class II extradiol dioxygenases) family.


Pssm-ID: 319902  Cd Length: 153  Bit Score: 36.48  E-value: 1.06e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 530368214  38 VTGsvwNLGrLNHVAIAVPDLEKAAAFYKNILGAQV-DNINAAVMDLKKKKIR 89
Cdd:cd07237    4 VTG---DQG-LGHVVLIVPDVDEALAFYTDVLGFRLsDEIRIPLPPGVTARLH 52
HPCD_N_class_II cd07266
N-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD); This subfamily ...
 44-73 1.59e-03

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: 35.85  E-value: 1.59e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 530368214  44 NLGRLNHVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:cd07266    1 DIIRLAHAELVVTDLAASREFYVDTLGLHV 30
GLOD5 cd07253
Human glyoxalase domain-containing protein 5 and similar proteins; Uncharacterized subfamily ...
 47-74 2.05e-03

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: 35.28  E-value: 2.05e-03
                         10        20
                 ....*....|....*....|....*...
gi 530368214  47 RLNHVAIAVPDLEKAAAFYKNILGAQVD 74
Cdd:cd07253    3 RLDHLVLTVKDIERTIDFYTKVLGMTVV 30
VOC_BsCatE_like_N cd07255
N-terminal of Bacillus subtilis CatE like protein; Uncharacterized subfamily of VOC ...
 47-73 3.18e-03

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: 34.98  E-value: 3.18e-03
                         10        20
                 ....*....|....*....|....*..
gi 530368214  47 RLNHVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:cd07255    2 RIGRVTLKVADLERQSAFYQNVIGLSV 28
PRK04101 PRK04101
metallothiol transferase FosB;
48-72 5.63e-03

metallothiol transferase FosB;


Pssm-ID: 179740  Cd Length: 139  Bit Score: 34.54  E-value: 5.63e-03
                         10        20
                 ....*....|....*....|....*
gi 530368214  48 LNHVAIAVPDLEKAAAFYKNILGAQ 72
Cdd:PRK04101   5 INHICFSVSNLEKSIEFYEKVLGAK 29
ED_TypeI_classII_N cd16360
N-terminal domain of type I, class II extradiol dioxygenases; This family contains the ...
 50-73 9.44e-03

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: 33.44  E-value: 9.44e-03
                         10        20
                 ....*....|....*....|....
gi 530368214  50 HVAIAVPDLEKAAAFYKNILGAQV 73
Cdd:cd16360    1 YAELGVPDLEKALEFYTDVLGLQV 24
 
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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