5M1B | pdb_00005m1b

Crystal structure of C-terminally tagged apo-UbiD from E. coli

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d5m1bc1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	automated matches	(Escherichia coli CFT073 ) [TaxId: 199310 ],	SCOPe (2.08)
C	d5m1bc2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	automated matches	automated matches	(Escherichia coli CFT073 ) [TaxId: 199310 ],	SCOPe (2.08)
B	d5m1bb1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	automated matches	(Escherichia coli CFT073 ) [TaxId: 199310 ],	SCOPe (2.08)
B	d5m1bb2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	automated matches	automated matches	(Escherichia coli CFT073 ) [TaxId: 199310 ],	SCOPe (2.08)
A	d5m1ba1	All beta proteins	Split barrel-like	FMN-binding split barrel	UbiD middle domain-like	automated matches	(Escherichia coli CFT073 ) [TaxId: 199310 ],	SCOPe (2.08)
A	d5m1ba2	Alpha and beta proteins (a+b)	UbiD C-terminal domain-like	UbiD C-terminal domain-like	automated matches	automated matches	(Escherichia coli CFT073 ) [TaxId: 199310 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Ras	e5m1bC1	A: a/b three-layered sandwiches	X: Small envelope protein M	H: Small envelope protein M	T: Small envelope protein M	F: Ras	ECOD (v294.1)
B	Ras	e5m1bB1	A: a/b three-layered sandwiches	X: Small envelope protein M	H: Small envelope protein M	T: Small envelope protein M	F: Ras	ECOD (v294.1)
A	Ras	e5m1bA1	A: a/b three-layered sandwiches	X: Small envelope protein M	H: Small envelope protein M	T: Small envelope protein M	F: Ras	ECOD (v294.1)

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	4-hydroxy-3-polyprenylbenzoate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity cation binding ion binding binding metal ion binding small molecule binding	small molecule biosynthetic process ketone metabolic process ubiquinone biosynthetic process quinone metabolic process biosynthetic process quinone biosynthetic process metabolic process cellular 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	IPR049383	3-octaprenyl-4-hydroxybenzoate carboxy-lyase-like, N-terminal domain	Domain
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

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.