1JC5 | pdb_00001jc5

Crystal Structure of Native Methylmalonyl-CoA Epimerase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1jc5a_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
B	d1jc5b_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
F	d1jc5f_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
E	d1jc5e_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
D	d1jc5d_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(Propionibacterium freudenreichii subsp. shermanii ) [TaxId: 1752 ],	SCOPe (2.08)
C	d1jc5c_	Alpha and beta proteins (a+b)	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Methylmalonyl-CoA epimerase	Methylmalonyl-CoA epimerase	(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)
A	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	8034325	3000739	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	3-dmu-9_3-mt	e1jc5A1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
B	3-dmu-9_3-mt	e1jc5B1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
F	3-dmu-9_3-mt	e1jc5F1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
E	3-dmu-9_3-mt	e1jc5E1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
D	3-dmu-9_3-mt	e1jc5D1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)
C	3-dmu-9_3-mt	e1jc5C1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: 3-dmu-9_3-mt	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
B	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
F	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
E	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
D	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)
C	3.10.180.10	Alpha Beta	Roll	2,3-Dihydroxybiphenyl 1,2-Dioxygenase	domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Methylmalonyl-CoA Epimerase	cation binding ion binding binding metal ion binding small molecule binding isomerase activity racemase and epimerase activity methylmalonyl-CoA epimerase activity catalytic activity	nucleoside phosphate metabolic process L-methylmalonyl-CoA metabolic process primary metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR017515	Methylmalonyl-CoA epimerase	Family
A, B, C, D, E A, B, C, D, E, F	IPR037523	Vicinal oxygen chelate (VOC), core domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR051785	Methylmalonyl-CoA/ethylmalonyl-CoA epimerase	Family
A, B, C, D, E A, B, C, D, E, F	IPR029068	Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	methylmalonyl-CoA epimerase M-CSA #33	Methylmalonyl-CoA epimerase is essential for the breakdown of odd-numbered fatty acids and the amino acids valine, isoleucine and methionine. It is present in many species of bacteria and animals. Defective activity in humans can result in severe acidosis and damage to the central nervous system.	Defined by 5 residues: HIS:A-12GLU:A-48GLN:A-65HIS:A-91GLU:A-141 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.1.99.1 (PDB Primary Data) Search M-CSA Motif + EC 5.1.99.1

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.