4KSA | pdb_00004ksa

Crystal Structure of Malonyl-CoA decarboxylase from Rhodopseudomonas palustris, Northeast Structural Genomics Consortium Target RpR127

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	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054010	3002263	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054011	3000403	SCOP2B (2022-06-29)
C	SCOP2 Family	Malonyl-CoA decarboxylase N-terminal domain	8046939	4005378	SCOP2 (2022-06-29)
C	SCOP2 Family	Malonyl-CoA decarboxylase C-terminal domain	8047063	4005426	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054010	3002263	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054011	3000403	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054011	3000403	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054010	3002263	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054011	3000403	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054010	3002263	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)
D	MCD_N	e4ksaD2	A: alpha superhelices	X: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	H: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	T: Mitochondrial malonyl-CoA decarboxylase helical domain	F: MCD_N	ECOD (1.6)
D	MCD	e4ksaD1	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: MCD	ECOD (1.6)
C	MCD_N	e4ksaC1	A: alpha superhelices	X: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	H: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	T: Mitochondrial malonyl-CoA decarboxylase helical domain	F: MCD_N	ECOD (1.6)
C	MCD	e4ksaC2	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: MCD	ECOD (1.6)
B	MCD_N	e4ksaB2	A: alpha superhelices	X: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	H: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	T: Mitochondrial malonyl-CoA decarboxylase helical domain	F: MCD_N	ECOD (1.6)
B	MCD	e4ksaB1	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: MCD	ECOD (1.6)
A	MCD_N	e4ksaA4	A: alpha superhelices	X: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	H: Mitochondrial malonyl-CoA decarboxylase helical domain (From Topology)	T: Mitochondrial malonyl-CoA decarboxylase helical domain	F: MCD_N	ECOD (1.6)
A	MCD	e4ksaA3	A: a+b three layers	X: Nat/Ivy	H: Acyl-CoA N-acyltransferases (Nat) (From Topology)	T: Acyl-CoA N-acyltransferases (Nat)	F: MCD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
D	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	CATH (4.3.0)
C	3.40.630.180	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase		CATH (4.3.0)
C	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
B	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
B	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	CATH (4.3.0)
A	3.40.630.180	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase		CATH (4.3.0)
A	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF17408	Malonyl-CoA decarboxylase N-terminal domain (MCD_N)	Malonyl-CoA decarboxylase N-terminal domain	This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that reg ...	This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK) [1].	Domain
A, B, C, D	PF05292	Malonyl-CoA decarboxylase C-terminal domain (MCD)	Malonyl-CoA decarboxylase C-terminal domain	This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that reg ...	This family consists of several eukaryotic malonyl-CoA decarboxylase (MLYCD) proteins. Malonyl-CoA, in addition to being an intermediate in the de novo synthesis of fatty acids, is an inhibitor of carnitine palmitoyltransferase I, the enzyme that regulates the transfer of long-chain fatty acyl-CoA into mitochondria, where they are oxidised. After exercise, malonyl-CoA decarboxylase participates with acetyl-CoA carboxylase in regulating the concentration of malonyl-CoA in liver and adipose tissue, as well as in muscle. Malonyl-CoA decarboxylase is regulated by AMP-activated protein kinase (AMPK) [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Malonyl-CoA decarboxylase	carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity malonyl-CoA decarboxylase activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process primary metabolic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007956	Malonyl-CoA decarboxylase, C-terminal	Domain
A, B, C, D	IPR038917	Malonyl-CoA decarboxylase	Family
A, B, C, D	IPR042303	Malonyl-CoA decarboxylase, C-terminal catalytic domain superfamily	Homologous Superfamily
A, B, C, D	IPR038351	Malonyl-CoA decarboxylase, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR035372	Malonyl-CoA decarboxylase, N-terminal	Domain

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.