3BIC | pdb_00003bic

Crystal structure of human methylmalonyl-CoA mutase

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e3bicB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: Abhydrolase_1	F:	ECOD (20:10:01)
A		e3bicA1	A: Profilin-like	X: sensor domains	H: sensor domains	T: Acyl-CoA_dh_1	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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
A, B	Methylmalonyl-CoA mutase, mitochondrial precursor	methylmalonyl-CoA mutase activity isomerase activity catalytic activity intramolecular transferase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding methylmalonyl-CoA mutase activity isomerase activity catalytic activity intramolecular transferase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding cation binding ion binding metal ion binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides modified amino acid binding	homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process fatty acid metabolic process homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process fatty acid metabolic process short-chain fatty acid metabolic process propionate metabolic process, methylmalonyl pathway monocarboxylic acid metabolic process propionate metabolic process lipid metabolic process positive regulation of molecular function regulation of molecular function positive regulation of hydrolase activity regulation of catalytic activity regulation of hydrolase activity biological regulation positive regulation of catalytic activity regulation of GTPase activity positive regulation of GTPase activity nucleoside phosphate metabolic process succinyl-CoA biosynthetic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process acyl-CoA metabolic process biosynthetic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process succinyl-CoA metabolic process phosphorus metabolic process developmental process multicellular organism development multicellular organismal process anatomical structure development post-embryonic development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006098	Methylmalonyl-CoA mutase, alpha chain, catalytic	Domain
A, B	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, B	IPR006099	Methylmalonyl-CoA mutase, alpha/beta chain, catalytic	Domain
A, B	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A, B	IPR006159	Methylmalonyl-CoA mutase, C-terminal	Domain
A, B	IPR058549	Methylmalonyl-CoA mutase, alpha/beta chain, conserved site	Conserved Site
A, B	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P22033	methylmalonic acidemia methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency inborn errors of metabolism obesity disorder atypical teratoid rhabdoid tumor lung cancer Methylmalonic Aciduria, mut(-) Type osteosarcoma psoriasis vitamin B12-unresponsive methylmalonic acidemia type mut0 cancer inherited organic acidemia ovarian cancer ulcerative colitis glioblastoma methylmalonic acidemia methylmalonic aciduria due to methylmalonyl-CoA mutase deficiency inborn errors of metabolism obesity disorder atypical teratoid rhabdoid tumor lung cancer Methylmalonic Aciduria, mut(-) Type osteosarcoma psoriasis vitamin B12-unresponsive methylmalonic acidemia type mut0 cancer inherited organic acidemia ovarian cancer ulcerative colitis glioblastoma large cell medulloblastoma pancreatic ductal adenocarcinoma vitamin B12-unresponsive methylmalonic acidemia type mut-

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.