2IDB
Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | UbiD middle domain-like | 8030320 | 4001862 | SCOP2 (2022-06-29) |
A | SCOP2 Family | UbiD C-terminal domain-like | 8030321 | 4000458 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | FMN-binding split barrel | 8042699 | 3000856 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | UbiD C-terminal domain-like | 8042700 | 3000341 | SCOP2 (2022-06-29) |
B | SCOP2B Superfamily | UbiD C-terminal domain-like | 8042700 | 3000341 | SCOP2B (2022-06-29) |
B | SCOP2B Superfamily | FMN-binding split barrel | 8042699 | 3000856 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | UbiD C-terminal domain-like | 8042700 | 3000341 | SCOP2B (2022-06-29) |
C | SCOP2B Superfamily | FMN-binding split barrel | 8042699 | 3000856 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | UbiD_2nd | e2idbA3 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: FMN-binding split barrel | F: UbiD_2nd | ECOD (1.6) |
A | UbiD_3rd | e2idbA2 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: UbiD C-terminal domain-like (From Topology) | T: UbiD C-terminal domain-like | F: UbiD_3rd | ECOD (1.6) |
A | UbiD_1st | e2idbA4 | A: a+b two layers | X: N-terminal subdomain in UbiD middle domain (From Topology) | H: N-terminal subdomain in UbiD middle domain (From Topology) | T: N-terminal subdomain in UbiD middle domain | F: UbiD_1st | ECOD (1.6) |
B | UbiD_2nd | e2idbB1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: FMN-binding split barrel | F: UbiD_2nd | ECOD (1.6) |
B | UbiD_3rd | e2idbB2 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: UbiD C-terminal domain-like (From Topology) | T: UbiD C-terminal domain-like | F: UbiD_3rd | ECOD (1.6) |
B | UbiD_1st | e2idbB3 | A: a+b two layers | X: N-terminal subdomain in UbiD middle domain (From Topology) | H: N-terminal subdomain in UbiD middle domain (From Topology) | T: N-terminal subdomain in UbiD middle domain | F: UbiD_1st | ECOD (1.6) |
C | UbiD_2nd | e2idbC1 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: FMN-binding split barrel | F: UbiD_2nd | ECOD (1.6) |
C | UbiD_3rd | e2idbC2 | A: a+b two layers | X: Alpha-lytic protease prodomain-like | H: UbiD C-terminal domain-like (From Topology) | T: UbiD C-terminal domain-like | F: UbiD_3rd | ECOD (1.6) |
C | UbiD_1st | e2idbC3 | A: a+b two layers | X: N-terminal subdomain in UbiD middle domain (From Topology) | H: N-terminal subdomain in UbiD middle domain (From Topology) | T: N-terminal subdomain in UbiD middle domain | F: UbiD_1st | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.40.1670.10 | Alpha Beta | 3-Layer(aba) Sandwich | UbiD C-terminal domain-like | UbiD C-terminal domain-like | CATH (4.3.0) |
A | 1.20.5.570 | Mainly Alpha | Up-down Bundle | Single alpha-helices involved in coiled-coils or other helix-helix interfaces | Single helix bin | CATH (4.3.0) |
B | 3.40.1670.10 | Alpha Beta | 3-Layer(aba) Sandwich | UbiD C-terminal domain-like | UbiD C-terminal domain-like | CATH (4.3.0) |
B | 1.20.5.570 | Mainly Alpha | Up-down Bundle | Single alpha-helices involved in coiled-coils or other helix-helix interfaces | Single helix bin | CATH (4.3.0) |
C | 3.40.1670.10 | Alpha Beta | 3-Layer(aba) Sandwich | UbiD C-terminal domain-like | UbiD C-terminal domain-like | CATH (4.3.0) |
C | 1.20.5.570 | Mainly Alpha | Up-down Bundle | Single alpha-helices involved in coiled-coils or other helix-helix interfaces | Single helix bin | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF20695 | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain (UbiD_N) | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain | This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes [1]. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+ [1]. This entry repr ... | Domain | |
PF20696 | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain (UbiD_C) | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain | This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes [1]. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+ [1]. This entry repr ... | Domain | |
PF01977 | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain (UbiD) | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain | This family has been characterised as 3-octaprenyl-4- hydroxybenzoate carboxy-lyase enzymes [1]. This enzyme catalyses the third reaction in ubiquinone biosynthesis. For optimal activity the carboxy-lase was shown to require Mn2+ [1]. This entry repr ... | Domain |