5VIT | pdb_00005vit

Crystal structure of a Pseudomonas malonate decarboxylase hetero-tetramer in complex with malonate

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth D]	KOW5_SPT5	e5vitD1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
G [auth S]	KOW5_SPT5	e5vitS1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
K [auth L]	KOW5_SPT5	e5vitL1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
O [auth Y]	KOW5_SPT5	e5vitY1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
D [auth E]	Brix	e5vitE1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
H [auth T]	Brix	e5vitT1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
L [auth M]	Brix	e5vitM1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
P [auth Z]	Brix	e5vitZ1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
F [auth R]	ACP	e5vitR1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: ACP	ECOD (v294.1)
J [auth K]	ACP	e5vitK1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: ACP	ECOD (v294.1)
N [auth X]	ACP	e5vitX1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ribosomal protein S5 domain 2-like	T: Ribosomal protein S5 domain 2-like	F: ACP	ECOD (v294.1)
B [auth C]	GDNF	e5vitC1	A: a/b three-layered sandwiches	X: RING/U-box-like	H: UDP-Glycosyltransferase/glycogen phosphorylase	T: UDP-Glycosyltransferase/glycogen phosphorylase	F: GDNF	ECOD (v294.1)
A	KOW5_SPT5	e5vitA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: KOW5_SPT5	ECOD (v294.1)
E [auth P]	Brix	e5vitP1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
M [auth V]	Brix	e5vitV1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)
I	Brix	e5vitI1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Brix	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth D], G [auth S], K [auth L], O [auth Y]	PF01039	Carboxyl transferase domain (Carboxyl_trans)	Carboxyl transferase domain	-	Family
D [auth E], H [auth T], L [auth M], P [auth Z]	PF06833	Malonate decarboxylase gamma subunit (MdcE)	Malonate decarboxylase gamma subunit	-	Family
A, E [auth P], I, M [auth V]	PF16957	Malonate decarboxylase, alpha subunit, transporter (Mal_decarbox_Al)	Malonate decarboxylase, alpha subunit, transporter	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], G [auth S], K [auth L], O [auth Y]	MdcD	transferase activity catalytic activity carboxy-lyase activity lyase activity carbon-carbon lyase activity	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 carbohydrate metabolic process	-
D [auth E], H [auth T], L [auth M], P [auth Z]	MdcE	-	carbohydrate metabolic process primary metabolic process metabolic process cellular process	-
B [auth C], F [auth R], J [auth K], N [auth X]	MdcC	phosphopantetheine-dependent carrier activity prosthetic group binding binding acyl carrier activity molecular carrier activity ACP phosphopantetheine attachment site binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm
A, E [auth P], I, M [auth V]	MdcA	transferase activity catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR017556	Biotin-independent malonate decarboxylase, beta subunit	Family
C [auth D], G [auth S], K [auth L], O [auth Y]	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain
D [auth E], H [auth T], L [auth M], P [auth Z]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
D [auth E], H [auth T], L [auth M], P [auth Z]	IPR009648	Biotin-dependent malonate decarboxylase, gamma subunit	Family
B [auth C], F [auth R], J [auth K], N [auth X]	IPR023439	Malonate decarboxylase/citrate lyase acyl carrier protein	Family
B [auth C], F [auth R], J [auth K], N [auth X]	IPR009662	Malonate decarboxylase delta subunit	Family
A, E [auth P], I, M [auth V]	IPR005777	Acetyl-S-ACP:malonate ACP transferase	Family
A, E [auth P], I, M [auth V]	IPR037171	NagB/RpiA transferase-like	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.