5REQ

Methylmalonyl-COA MUTASE, Y89F Mutant, substrate complex

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	d5reqc1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain	Methylmalonyl-CoA mutase alpha subunit, domain 1	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
C	d5reqc2	Alpha and beta proteins (a/b)	Flavodoxin-like	Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-binding domain	Methylmalonyl-CoA mutase alpha subunit, C-terminal domain	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
A	d5reqa1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain	Methylmalonyl-CoA mutase alpha subunit, domain 1	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
A	d5reqa2	Alpha and beta proteins (a/b)	Flavodoxin-like	Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-binding domain	Methylmalonyl-CoA mutase alpha subunit, C-terminal domain	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
B	d5reqb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain	Methylmalonyl-CoA mutase beta subunit, domain 1	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
B	d5reqb2	Alpha and beta proteins (a/b)	Flavodoxin-like	Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-binding domain	Methylmalonyl-CoA mutase beta subunit, C-terminal domain	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
D	d5reqd1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Cobalamin (vitamin B12)-dependent enzymes	Methylmalonyl-CoA mutase, N-terminal (CoA-binding) domain	Methylmalonyl-CoA mutase beta subunit, domain 1	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
D	d5reqd2	Alpha and beta proteins (a/b)	Flavodoxin-like	Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-binding domain	Methylmalonyl-CoA mutase beta subunit, C-terminal domain	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Cobalamin (vitamin B12)-binding domain	8044101	3001260	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8043843	3000609	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8043843	3000609	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cobalamin (vitamin B12)-binding domain	8044101	3001260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cobalamin (vitamin B12)-binding domain	8044102	3001260	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8043845	3000609	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cobalamin (vitamin B12)-dependent enzymes	8043845	3000609	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cobalamin (vitamin B12)-binding domain	8044102	3001260	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)
C	MM_CoA_mutase	e5reqC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MM_CoA_mutase	ECOD (1.6)
C	B12-binding	e5reqC2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: B12-binding	ECOD (1.6)
A	MM_CoA_mutase	e5reqA1	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	B12-binding	e5reqA2	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	e5reqB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MM_CoA_mutase	ECOD (1.6)
B	mmCoA_mut_beta	e5reqB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: mmCoA_mut_beta	ECOD (1.6)
D	MM_CoA_mutase	e5reqD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: MM_CoA_mutase	ECOD (1.6)
D	mmCoA_mut_beta	e5reqD2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: mmCoA_mut_beta	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.20.20.240	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Methylmalonyl-CoA mutase	CATH (4.3.0)
C	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)
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)
B	1.10.196.20	Mainly Alpha	Orthogonal Bundle	Regulator of G-protein Signalling 4	domain 1	CATH (4.3.0)
D	3.20.20.240	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Methylmalonyl-CoA mutase	CATH (4.3.0)
D	3.40.50.280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Cobalamin-binding domain	CATH (4.3.0)
D	1.10.196.20	Mainly Alpha	Orthogonal Bundle	Regulator of G-protein Signalling 4	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, C	PF01642	Methylmalonyl-CoA mutase (MM_CoA_mutase)	Methylmalonyl-CoA mutase	-	Family
B, D	PF01642	Methylmalonyl-CoA mutase (MM_CoA_mutase)	Methylmalonyl-CoA mutase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	PROTEIN (METHYLMALONYL-COA MUTASE ALPHA-SUBUNIT)	vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding methylmalonyl-CoA mutase activity isomerase activity catalytic activity intramolecular transferase activity cation binding ion binding metal ion binding	fatty acid metabolic process oxoacid metabolic process short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process propionate metabolic process, methylmalonyl pathway metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process propionate metabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
B, D	PROTEIN (METHYLMALONYL-COA MUTASE BETA-SUBUNIT)	vitamin binding binding cobalamin binding organic cyclic compound binding tetrapyrrole binding heterocyclic compound binding small molecule binding methylmalonyl-CoA mutase activity isomerase activity catalytic activity intramolecular transferase activity cation binding ion binding metal ion binding	fatty acid metabolic process lactate fermentation to propionate and acetate oxoacid metabolic process energy derivation by oxidation of organic compounds short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process generation of precursor metabolites and energy fermentation non-glycolytic fermentation metabolic process cellular process small molecule metabolic process fatty acid metabolic process lactate fermentation to propionate and acetate oxoacid metabolic process energy derivation by oxidation of organic compounds short-chain fatty acid metabolic process carboxylic acid metabolic process primary metabolic process organic acid metabolic process generation of precursor metabolites and energy fermentation non-glycolytic fermentation metabolic process cellular process small molecule metabolic process monocarboxylic acid metabolic process propionate metabolic process lipid metabolic process propionate metabolic process, methylmalonyl pathway	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR006099	Methylmalonyl-CoA mutase, alpha/beta chain, catalytic	Domain
A, C	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A, C	IPR006098	Methylmalonyl-CoA mutase, alpha chain, catalytic	Domain
A, C	IPR006159	Methylmalonyl-CoA mutase, C-terminal	Domain
A, C	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, C	IPR016176	Cobalamin (vitamin B12)-dependent enzyme, catalytic	Homologous Superfamily
B, D	IPR006099	Methylmalonyl-CoA mutase, alpha/beta chain, catalytic	Domain
B, D	IPR024067	Methylmalonyl-CoA mutase small subunit, N-terminal	Homologous Superfamily
B, D	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
B, D	IPR004608	Methylmalonyl-CoA mutase, small subunit	Family
B, D	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.