4R3U | pdb_00004r3u

Crystal structure of 2-Hydroxyisobutyryl-CoA Mutase

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2 Family	Cobalamin (vitamin B12)-binding domain	8083295	4003680	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Cobalamin (vitamin B12)-binding domain	8083296	3001260	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Cobalamin (vitamin B12)-binding domain	8083296	3001260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8097956	3000609	SCOP2B (2022-06-29)
A	SCOP2 Family	Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain	8097955	4003330	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8097956	3000609	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)
D	B12-binding	e4r3uD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
C	B12-binding	e4r3uC1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
B	MM_CoA_mutase	e4r3uB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MM_CoA_mutase	ECOD (1.6)
A	MM_CoA_mutase	e4r3uA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MM_CoA_mutase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
C	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
B	3.20.20.240	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Methylmalonyl-CoA mutase	CATH (4.3.0)
A	3.20.20.240	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Methylmalonyl-CoA mutase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF02310	B12 binding domain (B12-binding)	B12 binding domain	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, ...	This domain binds to B12 (adenosylcobamide)[1-3], it is found in several enzymes, such as glutamate mutase Swiss:Q05488, methionine synthase Swiss:Q99707 and methylmalonyl-CoA mutase Swiss:P22033. It contains a conserved DxHxxGx(41)SxVx(26)GG motif, which is important for B12 binding [2].	Domain
A, B	PF01642	Methylmalonyl-CoA mutase (MM_CoA_mutase)	Methylmalonyl-CoA mutase	The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rear ...	The enzyme methylmalonyl-CoA mutase is a member of a class of enzymes that uses coenzyme B12 (adenosylcobalamin) as a cofactor. The enzyme induces the formation of an adenosyl radical from the cofactor. This radical then initiates a free-radical rearrangement of its substrate, succinyl-CoA, to methylmalonyl-CoA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	2-hydroxyisobutyryl-CoA mutase small subunit	isomerase activity catalytic activity vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding	-	-
A, B	2-hydroxyisobutyryl-CoA mutase large subunit	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding methylmalonyl-CoA mutase activity isomerase activity catalytic activity intramolecular transferase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, D	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
C, D	IPR006159	Methylmalonyl-CoA mutase, C-terminal	Domain
C, D	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, B	IPR006099	Methylmalonyl-CoA mutase, alpha/beta chain, catalytic	Domain
A, B	IPR006098	Methylmalonyl-CoA mutase, alpha chain, catalytic	Domain
A, B	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily

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.