6H6V

Structure of the UbiD-class enzyme HmfF from Pelotomaculum thermopropionicum in complex with FMN

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	e6h6vA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
A	UbiD_3rd	e6h6vA2	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	e6h6vA1	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	e6h6vB3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
B	UbiD_3rd	e6h6vB2	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	e6h6vB1	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	e6h6vC3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
C	UbiD_3rd	e6h6vC2	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	e6h6vC1	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	e6h6vD3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
D	UbiD_3rd	e6h6vD1	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	e6h6vD2	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)
E	UbiD_2nd	e6h6vE3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
E	UbiD_3rd	e6h6vE1	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)
E	UbiD_1st	e6h6vE2	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)
F	UbiD_2nd	e6h6vF3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD_2nd	ECOD (1.6)
F	UbiD_3rd	e6h6vF1	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)
F	UbiD_1st	e6h6vF2	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, 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	3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	ether metabolic process oxoacid metabolic process ferulate metabolic process organic hydroxy compound metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process phenol-containing compound metabolic process olefinic compound metabolic process metabolic process small molecule metabolic process cellular process monocarboxylic acid metabolic process phenylpropanoid catabolic process ether metabolic process oxoacid metabolic process ferulate metabolic process organic hydroxy compound metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process phenol-containing compound metabolic process olefinic compound metabolic process metabolic process small molecule metabolic process cellular process monocarboxylic acid metabolic process phenylpropanoid catabolic process phenylpropanoid metabolic process catabolic process benzene-containing compound metabolic process organic acid catabolic process secondary metabolic process cellular catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process olefinic compound catabolic process small molecule catabolic process cinnamic acid catabolic process cinnamic acid metabolic process small molecule biosynthetic process cellular biosynthetic process ubiquinone biosynthetic process quinone metabolic process cellular ketone metabolic process biosynthetic process quinone biosynthetic process ubiquinone metabolic process ketone biosynthetic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

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	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

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.