6DA6

Crystal structure of the TtnD decarboxylase from the tautomycetin biosynthesis pathway of Streptomyces griseochromogenes, apo form at 2.6 A resolution (P212121)

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	UbiD_2nd	e6da6A2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
A	UbiD_3rd	e6da6A3	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	e6da6A4	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	e6da6B2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
B	UbiD_3rd	e6da6B1	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	e6da6B3	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	e6da6C2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
C	UbiD_3rd	e6da6C3	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	e6da6C4	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)
D	UbiD_2nd	e6da6D2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
D	UbiD_3rd	e6da6D3	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)
D	UbiD_1st	e6da6D4	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	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
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	UbiD-like decarboxylase	cation binding ion binding binding metal ion binding small molecule binding carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR049383	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, N-terminal domain	Domain
A, B, C, D	IPR032903	Ferulic acid decarboxylase-like	Family
A, B, C, D	IPR002830	UbiD decarboxylyase family	Family
A, B, C, D	IPR049381	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, C-terminal domain	Domain
A, B, C, D	IPR048304	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-likw, Rift-related domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.