5VJ1 | pdb_00005vj1

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

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	CoA_trans	e5vj1A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: CoA_trans	ECOD (1.6)
A	UNK_F_TYPE	e5vj1A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: UNK_F_TYPE	ECOD (1.6)
E [auth I]	CoA_trans	e5vj1I1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: CoA_trans	ECOD (1.6)
E [auth I]	UNK_F_TYPE	e5vj1I2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: UNK_F_TYPE	ECOD (1.6)
F [auth K]	UNK_F_TYPE	e5vj1K1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: UNK_F_TYPE	ECOD (1.6)
B [auth C]	UNK_F_TYPE	e5vj1C1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: UNK_F_TYPE	ECOD (1.6)
C [auth D]	Carboxyl_trans_N	e5vj1D1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_N	ECOD (1.6)
G [auth L]	Carboxyl_trans_N	e5vj1L1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_N	ECOD (1.6)
D [auth E]	ACCA	e5vj1E1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: ACCA	ECOD (1.6)
H [auth M]	ACCA	e5vj1M1	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: ACCA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth D]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)
G [auth L]	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth I]	PF16957	Malonate decarboxylase, alpha subunit, transporter (Mal_decarbox_Al)	Malonate decarboxylase, alpha subunit, transporter	-	Family
B [auth C], F [auth K]	PF06857	Malonate decarboxylase delta subunit (MdcD) (ACP)	Malonate decarboxylase delta subunit (MdcD)	-	Family
C [auth D], G [auth L]	PF01039	Carboxyl transferase domain (Carboxyl_trans)	Carboxyl transferase domain	-	Family
D [auth E], H [auth M]	PF06833	Malonate decarboxylase gamma subunit (MdcE)	Malonate decarboxylase gamma subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth I]	MdcA	transferase activity catalytic activity	-	-
B [auth C], F [auth K]	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
C [auth D], G [auth L]	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 M]	MdcE	-	carbohydrate metabolic process primary metabolic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth I]	IPR005777	Acetyl-S-ACP:malonate ACP transferase	Family
A, E [auth I]	IPR037171	NagB/RpiA transferase-like	Homologous Superfamily
B [auth C], F [auth K]	IPR023439	Malonate decarboxylase/citrate lyase acyl carrier protein	Family
B [auth C], F [auth K]	IPR009662	Malonate decarboxylase delta subunit	Family
C [auth D], G [auth L]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
C [auth D], G [auth L]	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
C [auth D], G [auth L]	IPR017556	Biotin-independent malonate decarboxylase, beta subunit	Family
C [auth D], G [auth L]	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain
D [auth E], H [auth M]	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
D [auth E], H [auth M]	IPR009648	Biotin-dependent malonate decarboxylase, gamma subunit	Family

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.