5M1D

Crystal structure of N-terminally tagged UbiD from E. coli reconstituted with prFMN cofactor

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5m1da1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d5m1da2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d5m1db1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d5m1db2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d5m1dc1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d5m1dc2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	automated matches	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FMN-binding split barrel	8042699	3000856	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UbiD C-terminal domain-like	8042700	3000341	SCOP2B (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	FMN-binding split barrel	8042699	3000856	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	UbiD C-terminal domain-like	8042700	3000341	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	PF01977	e5m1dA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
A	PF20696	e5m1dA1	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	e5m1dA3	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	e5m1dB2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
B	PF20696	e5m1dB1	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	e5m1dB3	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	e5m1dC2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PF01977	ECOD (1.6)
C	PF20696	e5m1dC1	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	e5m1dC3	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)

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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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	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	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	3-octaprenyl-4-hydroxybenzoate carboxy-lyase	binding nucleotide binding prenyl-FMNH2 binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding manganese ion binding transition metal ion binding binding nucleotide binding prenyl-FMNH2 binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding manganese ion binding transition metal ion binding metal ion binding 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein binding	oxoacid metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process ubiquinone biosynthetic process quinone metabolic process chorismate metabolic process organic substance metabolic process cellular ketone metabolic process biosynthetic process quinone biosynthetic process organic substance biosynthetic process oxoacid metabolic process small molecule biosynthetic process cellular biosynthetic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process organic acid metabolic process ubiquinone biosynthetic process quinone metabolic process chorismate metabolic process organic substance metabolic process cellular ketone metabolic process biosynthetic process quinone biosynthetic process organic substance biosynthetic process ubiquinone biosynthetic process from chorismate small molecule metabolic process metabolic process cellular process ubiquinone metabolic process ketone biosynthetic process cellular component organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR023677	UbiD decarboxylyase, bacteria	Family
A, B, C	IPR002830	UbiD decarboxylyase family	Family
A, B, C	IPR049381	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, C-terminal domain	Domain
A, B, C	IPR048304	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-likw, Rift-related domain	Domain
A, B, C	IPR049383	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, N-terminal 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.