2IDB | pdb_00002idb

Crystal Structure of 3-octaprenyl-4-hydroxybenzoate decarboxylase (UbiD) from Escherichia coli, Northeast Structural Genomics Target ER459.

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)
C	d2idbc1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d2idbc2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	UbiD C-terminal domain-like	3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2idbb1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d2idbb2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	UbiD C-terminal domain-like	3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2idba1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d2idba2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	UbiD C-terminal domain-like	3-octaprenyl-4-hydroxybenzoate carboxy-lyase UbiD	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Staphylokinase	e2idbC2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
C	zf-MYND	e2idbC1	A: alpha bundles	X: jelly-roll	H: Double-stranded beta-helix	T: Double-stranded beta-helix	F: zf-MYND	ECOD (develop294)
B	Staphylokinase	e2idbB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Staphylokinase	ECOD (develop294)
B	ADAM_CR	e2idbB1	A: alpha bundles	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: ADAM_CR	ECOD (develop294)
A	UbiD_C	e2idbA2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: UbiD C-terminal domain-like	T: UbiD C-terminal domain-like	F: UbiD_C	ECOD (develop294)
A	UbiD	e2idbA3	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: UbiD	ECOD (develop294)
A	Internalin_N	e2idbA4	A: alpha bundles	X: Single-stranded right-handed beta-helix	H: Leucine-rich repeats	T: Leucine-rich repeats	F: Internalin_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)

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	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	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	3-octaprenyl-4-hydroxybenzoate carboxy-lyase	prenyl-FMNH2 binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding manganese ion binding transition metal ion binding metal ion binding prenyl-FMNH2 binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding manganese ion binding transition metal ion binding metal ion binding 4-hydroxy-3-polyprenylbenzoate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity identical protein binding protein binding	cellular component organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular process cellular component organization or biogenesis small molecule biosynthetic process ketone metabolic process ubiquinone biosynthetic process quinone metabolic process 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 process cellular component organization or biogenesis small molecule biosynthetic process ketone metabolic process ubiquinone biosynthetic process quinone metabolic process biosynthetic process quinone biosynthetic process metabolic process small molecule metabolic process ubiquinone metabolic process ketone biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR048304	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, Rift-related domain	Domain
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	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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.