8GJU | pdb_00008gju

Crystal structure of human methylmalonyl-CoA mutase (MMUT) in complex with methylmalonic acidemia type A protein (MMAA), coenzyme A, and GDP

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056302	3002018	SCOP2B (2022-06-29)
G [auth B]	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056302	3002018	SCOP2B (2022-06-29)
F [auth A]	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056302	3002018	SCOP2B (2022-06-29)
B [auth F]	SCOP2B Superfamily	Simibi-like P-loop NTPases	8056302	3002018	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 [auth D]		e8gjuD1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Cullin_AB	F:	ECOD (20:10:01)
G [auth B]		e8gjuB1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: WD40,CAF1C_H4-bd	F:	ECOD (20:10:01)
F [auth A]		e8gjuA1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Cullin_AB	F:	ECOD (20:10:01)
B [auth F]		e8gjuF1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Cullin_AB	F:	ECOD (20:10:01)
C [auth J]		e8gjuJ1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: WD40,CAF1C_H4-bd	F:	ECOD (20:10:01)
D [auth K]		e8gjuK1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Cullin_AB	F:	ECOD (20:10:01)
H		e8gjuH1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Cullin_AB	F:	ECOD (20:10:01)
E [auth L]		e8gjuL1	A: Family A G protein-coupled receptor-like	X: Family A G protein-coupled receptor-like	H: Family A G protein-coupled receptor-like	T: Cullin_AB	F:	ECOD (20:10:01)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D], B [auth F], F [auth A], G [auth B]	PF03308	Methylmalonyl Co-A mutase-associated GTPase MeaB (MeaB)	Methylmalonyl Co-A mutase-associated GTPase MeaB	Family members were previously thought to be ArgK proteins acting as ATPase enzymes and kinases. They are now believed to be methylmalonyl Co-A mutase-associated GTPase MeaB. Structural studies of MeaB and the human ortholog (methylmalonyl associated ...	Family members were previously thought to be ArgK proteins acting as ATPase enzymes and kinases. They are now believed to be methylmalonyl Co-A mutase-associated GTPase MeaB. Structural studies of MeaB and the human ortholog (methylmalonyl associated protein A) MMAA, reveal alpha-helical domains at the N- and C-termini as well as a Ras-like GTPase domain. Mutational analysis of MeaB, show prohibited growth in Methylobacterium due to the inability to convert methylmalonyl-CoA to succinyl-CoA caused by an inactive form of methylmalonyl-CoA mutatase (mcm). In humans, mutations in (MMAA) are associated with the fatal disease methylmalonyl aciduria [1].	Domain
C [auth J], D [auth K], E [auth L], H	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
C [auth J], D [auth K], E [auth L], H	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 [auth D], B [auth F], F [auth A], G [auth B]	Methylmalonic aciduria type A protein, mitochondrial	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity molecular carrier activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding identical protein binding protein binding binding protein homodimerization activity protein dimerization activity molecular carrier activity guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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 catalytic activity	cobalamin metabolic process tetrapyrrole metabolic process metabolic process cellular process nucleoside phosphate metabolic process succinyl-CoA biosynthetic process primary metabolic 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 cobalamin metabolic process tetrapyrrole metabolic process metabolic process cellular process nucleoside phosphate metabolic process succinyl-CoA biosynthetic process primary metabolic 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 sulfur compound metabolic process small molecule metabolic process succinyl-CoA metabolic process phosphorus metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
C [auth J], D [auth K], E [auth L], H	Methylmalonyl-CoA mutase, mitochondrial	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 [auth D], B [auth F], F [auth A], G [auth B]	IPR005129	SIMIBI class G3E GTPase, ArgK/MeaB	Family
A [auth D], B [auth F], F [auth A], G [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth J], D [auth K], E [auth L], H	IPR006098	Methylmalonyl-CoA mutase, alpha chain, catalytic	Domain
C [auth J], D [auth K], E [auth L], H	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
C [auth J], D [auth K], E [auth L], H	IPR006099	Methylmalonyl-CoA mutase, alpha/beta chain, catalytic	Domain
C [auth J], D [auth K], E [auth L], H	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
C [auth J], D [auth K], E [auth L], H	IPR006159	Methylmalonyl-CoA mutase, C-terminal	Domain
C [auth J], D [auth K], E [auth L], H	IPR058549	Methylmalonyl-CoA mutase, alpha/beta chain, conserved site	Conserved Site
C [auth J], D [auth K], E [auth L], H	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth D], B [auth F], F [auth A], G [auth B]	Pharos: Q8IVH4	vitamin B12-responsive methylmalonic acidemia type cblA methylmalonic acidemia homocystinuria inherited organic acidemia medulloblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia Hyperammonemia intellectual disability pancreatic ductal adenocarcinoma Sjogren syndrome inborn errors of metabolism large cell medulloblastoma pancreatic intraductal papillary-mucinous carcinoma subependymal giant cell astrocytoma
C [auth J], D [auth K], E [auth L], H	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.