7AE7

Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form, with truncated ShVdcD (V59X)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF01977	e7ae7A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
A	PF20696	e7ae7A2	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: PF20696	ECOD (1.6)
A	PF20695	e7ae7A3	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: PF20695	ECOD (1.6)
B	PF01977	e7ae7B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
B	PF20696	e7ae7B2	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: PF20696	ECOD (1.6)
B	PF20695	e7ae7B3	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: PF20695	ECOD (1.6)
E	PF01977	e7ae7E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
E	PF20696	e7ae7E2	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: PF20696	ECOD (1.6)
E	PF20695	e7ae7E3	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: PF20695	ECOD (1.6)
F	PF01977	e7ae7F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
F	PF20696	e7ae7F2	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: PF20696	ECOD (1.6)
F	PF20695	e7ae7F3	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: PF20695	ECOD (1.6)
C	PF01977	e7ae7C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
C	PF20696	e7ae7C2	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: PF20696	ECOD (1.6)
C	PF20695	e7ae7C3	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: PF20695	ECOD (1.6)
D	PF01977	e7ae7D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
D	PF20696	e7ae7D2	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: PF20696	ECOD (1.6)
D	PF20695	e7ae7D3	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: PF20695	ECOD (1.6)
G [auth a]	F_UNCLASSIFIED	e7ae7a1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
H [auth b]	F_UNCLASSIFIED	e7ae7b1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
I [auth c]	F_UNCLASSIFIED	e7ae7c1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
J [auth d]	F_UNCLASSIFIED	e7ae7d1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
K [auth e]	F_UNCLASSIFIED	e7ae7e1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)
L [auth f]	F_UNCLASSIFIED	e7ae7f1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: F_UNCLASSIFIED	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	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 ...	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 represents the N-terminal domain.	Domain
A, B, C, D, E A, B, C, D, E, F	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 ...	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 represents the C-terminal domain.	Domain
A, B, C, D, E A, B, C, D, E, F	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 ...	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 represents the central RIFT-related domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Phenolic acid decarboxylase	4-hydroxybenzoate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity cation binding ion binding binding metal ion binding small molecule binding protocatechuate decarboxylase activity	response to stimulus response to chemical response to toxic substance	-
G [auth a], H [auth b], I [auth c], J [auth d], K [auth e], G [auth a], H [auth b], I [auth c], J [auth d], K [auth e], L [auth f]	Protein ShdD	-	response to stimulus response to chemical response to toxic substance	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR049383	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, N-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR032902	Phenolic acid decarboxylase subunit C	Family
A, B, C, D, E A, B, C, D, E, F	IPR002830	UbiD decarboxylyase family	Family
A, B, C, D, E A, B, C, D, E, F	IPR049381	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR048304	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-likw, Rift-related domain	Domain
G [auth a], H [auth b], I [auth c], J [auth d], K [auth e], G [auth a], H [auth b], I [auth c], J [auth d], K [auth e], L [auth f]	IPR047707	Phenolic acid decarboxylase VdcD-like	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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7AE7

Structure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form, with truncated ShVdcD (V59X)

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage