4F0X | pdb_00004f0x

Crystal structure of human Malonyl-CoA Decarboxylase (Peroxisomal Isoform)

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Malonyl-CoA decarboxylase N-terminal domain-like	8054014	3002263	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Acyl-CoA N-acyltransferases (Nat)	8054015	3000403	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	MCD_N	e4f0xA1	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	e4f0xA2	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	e4f0xB4	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	e4f0xB3	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	e4f0xC4	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	e4f0xC3	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)
D	MCD_N	e4f0xD4	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	e4f0xD3	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)
E	MCD_N	e4f0xE4	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)
E	MCD	e4f0xE3	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)
F	MCD_N	e4f0xF4	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)
F	MCD	e4f0xF3	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)
G	MCD_N	e4f0xG4	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)
G	MCD	e4f0xG3	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)
H	MCD_N	e4f0xH4	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)
H	MCD	e4f0xH3	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)
A	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
A	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	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)
C	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
C	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	CATH (4.3.0)
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)
E	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
E	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	CATH (4.3.0)
F	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
F	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	CATH (4.3.0)
G	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
G	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	CATH (4.3.0)
H	1.20.140.90	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
H	3.40.630.150	Alpha Beta	3-Layer(aba) Sandwich	Aminopeptidase	Malonyl-CoA decarboxylase, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	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, E A, B, C, D, E, F, G, H	Malonyl-CoA decarboxylase, mitochondrial	carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity malonyl-CoA decarboxylase activity identical protein binding protein binding binding	nucleoside phosphate 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 metabolic process cellular process sulfur compound metabolic process small molecule metabolic process amide metabolic process thioester metabolic process nucleoside phosphate 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 metabolic process cellular process sulfur compound metabolic process small molecule metabolic process amide metabolic process thioester metabolic process phosphorus metabolic process regulation of cellular process oxoacid metabolic process ketone metabolic process regulation of lipid metabolic process positive regulation of biological process organic acid metabolic process regulation of primary metabolic process regulation of fatty acid oxidation positive regulation of metabolic process fatty acid oxidation regulation of small molecule metabolic process positive regulation of lipid metabolic process lipid oxidation positive regulation of cellular process positive regulation of fatty acid metabolic process fatty acid metabolic process regulation of biological process biological regulation carboxylic acid metabolic process lipid modification regulation of ketone metabolic process positive regulation of fatty acid oxidation regulation of fatty acid metabolic process monocarboxylic acid metabolic process positive regulation of small molecule metabolic process regulation of metabolic process lipid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process lipid biosynthetic process organic acid biosynthetic process fatty acid biosynthetic process carboxylic acid biosynthetic process biosynthetic process response to stimulus response to stress response to ischemia catabolic process malonyl-CoA metabolic process organophosphate catabolic process nucleoside phosphate catabolic process purine-containing compound catabolic process nucleobase-containing compound catabolic process sulfur compound catabolic process malonyl-CoA catabolic process response to nutrient levels response to chemical response to nutrient thioester biosynthetic process acetyl-CoA metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process amide biosynthetic process nucleobase-containing compound biosynthetic process acetyl-CoA biosynthetic process sulfur compound biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process monosaccharide metabolic process carbohydrate metabolic process hexose metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process glucose metabolic process organic acid catabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process fatty acid beta-oxidation lipid catabolic process regulation of fatty acid beta-oxidation regulation of catabolic process regulation of lipid catabolic process fatty acid catabolic process small molecule catabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle peroxisome microbody cytosol peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle peroxisome microbody cytosol peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen mitochondrial matrix

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E A, B, C, D, E, F, G, H	Pharos: O95822	malonic aciduria Hyperammonemia pancreatic ductal adenocarcinoma intellectual disability psoriasis tuberculosis

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.