3U9S

Crystal structure of P. aeruginosa 3-methylcrotonyl-CoA carboxylase (MCC) 750 kD holoenzyme, CoA complex

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)
C	PccA_like	e3u9sC3	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA_like	ECOD (1.6)
C	ATP-grasp	e3u9sC1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
C	Biotin_carb_C	e3u9sC2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
C	Biotin_carb_N	e3u9sC4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
G	PccA_like	e3u9sG3	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA_like	ECOD (1.6)
G	ATP-grasp	e3u9sG1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
G	Biotin_carb_C	e3u9sG2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
G	Biotin_carb_N	e3u9sG4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
A	PccA_like	e3u9sA3	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA_like	ECOD (1.6)
A	ATP-grasp	e3u9sA1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
A	Biotin_carb_C	e3u9sA2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
A	Biotin_lipoyl	e3u9sA5	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl	ECOD (1.6)
A	Biotin_carb_N	e3u9sA4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
E	PccA_like	e3u9sE3	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA_like	ECOD (1.6)
E	ATP-grasp	e3u9sE1	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
E	Biotin_carb_C	e3u9sE2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
E	Biotin_carb_N	e3u9sE4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
I	PccA_like	e3u9sI2	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA_like	ECOD (1.6)
I	ATP-grasp	e3u9sI6	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
I	Biotin_carb_C	e3u9sI1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
I	Biotin_carb_N	e3u9sI5	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
K	PccA_like	e3u9sK2	A: a+b two layers	X: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related (From Homology)	H: Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related	T: Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit	F: PccA_like	ECOD (1.6)
K	ATP-grasp	e3u9sK6	A: a+b complex topology	X: Protein kinase/SAICAR synthase/ATP-grasp (From Homology)	H: Protein kinase/SAICAR synthase/ATP-grasp	T: ATP-grasp	F: ATP-grasp	ECOD (1.6)
K	Biotin_carb_C	e3u9sK1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (1.6)
K	Biotin_carb_N	e3u9sK5	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
B	Carboxyl_trans_C	e3u9sB5	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)
D	Carboxyl_trans_C	e3u9sD5	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)
F	Carboxyl_trans_C	e3u9sF5	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)
H	Carboxyl_trans_C	e3u9sH5	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)
J	Carboxyl_trans_C	e3u9sJ5	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)
L	Carboxyl_trans_C	e3u9sL5	A: a/b three-layered sandwiches	X: ClpP/crotonase (From Topology)	H: ClpP/crotonase (From Topology)	T: ClpP/crotonase	F: Carboxyl_trans_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	3.30.700.40	Alpha Beta	2-Layer Sandwich	Glycoprotein, Type 4 Pilin		CATH (4.3.0)
G	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
G	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
G	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
G	3.30.700.40	Alpha Beta	2-Layer Sandwich	Glycoprotein, Type 4 Pilin		CATH (4.3.0)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.30.700.40	Alpha Beta	2-Layer Sandwich	Glycoprotein, Type 4 Pilin		CATH (4.3.0)
A	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.3.0)
E	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
E	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
E	3.30.700.40	Alpha Beta	2-Layer Sandwich	Glycoprotein, Type 4 Pilin		CATH (4.3.0)
I	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
I	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
I	3.30.700.40	Alpha Beta	2-Layer Sandwich	Glycoprotein, Type 4 Pilin		CATH (4.3.0)
K	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
K	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
K	3.30.700.40	Alpha Beta	2-Layer Sandwich	Glycoprotein, Type 4 Pilin		CATH (4.3.0)
B	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
D	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
F	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
H	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
J	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)
L	3.90.226.10	Alpha Beta	Alpha-Beta Complex	2-enoyl-CoA Hydratase	Chain A, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K	PF00364	Biotin-requiring enzyme (Biotin_lipoyl)	Biotin-requiring enzyme	This family covers two Prosite entries, the conserved lysine residue binds biotin in one group and lipoic acid in the other. Note that the HMM does not currently recognise the Glycine cleavage system H proteins.	Domain
A, C, E, G, I A, C, E, G, I, K	PF02786	Carbamoyl-phosphate synthase L chain, ATP binding domain (CPSase_L_D2)	Carbamoyl-phosphate synthase L chain, ATP binding domain	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The c ...	Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines [2]. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesise carbamoyl phosphate. See Pfam:PF00988. The small chain has a GATase domain in the carboxyl terminus. See Pfam:PF00117. The ATP binding domain (this one) has an ATP-grasp fold.	Domain
A, C, E, G, I A, C, E, G, I, K	PF00289	Biotin carboxylase, N-terminal domain (Biotin_carb_N)	Biotin carboxylase, N-terminal domain	This domain is structurally related to the PreATP-grasp domain. The family contains the N-terminus of biotin carboxylase enzymes [1,3], and propionyl-CoA carboxylase A chain [2].	Domain
A, C, E, G, I A, C, E, G, I, K	PF02785	Biotin carboxylase C-terminal domain (Biotin_carb_C)	Biotin carboxylase C-terminal domain	Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are i ...	Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference [1] are in this C-terminal domain.	Domain
A, C, E, G, I A, C, E, G, I, K	PF21139	Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain (MCC_alpha_BT)	Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain	This domain is found in the biotin-containing alpha subunit of the Methylcrotonyl-CoA carboxylase complex (MCC) from Pseudomonas aeruginosa and in similar bacterial proteins. MCC is essential for the metabolism of leucine. The alpha subunit is organi ...	This domain is found in the biotin-containing alpha subunit of the Methylcrotonyl-CoA carboxylase complex (MCC) from Pseudomonas aeruginosa and in similar bacterial proteins. MCC is essential for the metabolism of leucine. The alpha subunit is organised into the N-terminal biotin carboxylase (BC), the C-terminal biotin carboxyl carrier protein (BCCP) domains, and a domain that mediates BC-CT interactions (BT domain, this entry). This domain shows a central alpha-helix surrounded by a seven-stranded, highly- twisted anti-parallel beta-sheet, with an overall structure that has great similarity with the beta-barrel of the BT domain of the human MCC [1].	Domain
B, D, F, H, J B, D, F, H, J, L	PF01039	Carboxyl transferase domain (Carboxyl_trans)	Carboxyl transferase domain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K	Methylcrotonyl-CoA carboxylase, alpha-subunit	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding CoA carboxylase activity methylcrotonoyl-CoA carboxylase activity ligase activity, forming carbon-carbon bonds catalytic activity ligase activity cation binding metal ion binding	pyruvate family amino acid metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process alpha-amino acid metabolic process pyruvate family amino acid catabolic process cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process branched-chain amino acid metabolic process pyruvate family amino acid metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process alpha-amino acid metabolic process pyruvate family amino acid catabolic process cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process branched-chain amino acid metabolic process amino acid catabolic process L-leucine metabolic process organonitrogen compound catabolic process L-leucine catabolic process organonitrogen compound metabolic process cellular metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process isoprenoid catabolic process lipid catabolic process cellular lipid catabolic process cellular lipid metabolic process lipid metabolic process isoprenoid metabolic process hydrocarbon catabolic process terpene metabolic process hydrocarbon metabolic process terpene catabolic process	protein-containing complex catalytic complex methylcrotonoyl-CoA carboxylase complex
B, D, F, H, J B, D, F, H, J, L	Methylcrotonyl-CoA carboxylase, beta-subunit	CoA carboxylase activity methylcrotonoyl-CoA carboxylase activity ligase activity, forming carbon-carbon bonds catalytic activity ligase activity	pyruvate family amino acid metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process alpha-amino acid metabolic process pyruvate family amino acid catabolic process cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process branched-chain amino acid metabolic process pyruvate family amino acid metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process alpha-amino acid metabolic process pyruvate family amino acid catabolic process cellular catabolic process organic substance metabolic process carboxylic acid catabolic process small molecule metabolic process branched-chain amino acid metabolic process amino acid catabolic process L-leucine metabolic process organonitrogen compound catabolic process L-leucine catabolic process organonitrogen compound metabolic process cellular metabolic process carboxylic acid metabolic process L-amino acid catabolic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process isoprenoid catabolic process lipid catabolic process cellular lipid catabolic process cellular lipid metabolic process lipid metabolic process isoprenoid metabolic process	protein-containing complex catalytic complex methylcrotonoyl-CoA carboxylase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K	IPR005481	Biotin carboxylase-like, N-terminal domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR011761	ATP-grasp fold	Domain
A, C, E, G, I A, C, E, G, I, K	IPR011764	Biotin carboxylation domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR005482	Biotin carboxylase, C-terminal	Domain
A, C, E, G, I A, C, E, G, I, K	IPR005479	Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR048429	Methylcrotonyl-CoA carboxylase, alpha-subunit, BT domain	Domain
A, C, E, G, I A, C, E, G, I, K	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR011053	Single hybrid motif	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K	IPR000089	Biotin/lipoyl attachment	Domain
B, D, F, H, J B, D, F, H, J, L	IPR011763	Acetyl-coenzyme A carboxyltransferase, C-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
B, D, F, H, J B, D, F, H, J, L	IPR045190	Methylcrotonoyl-CoA carboxylase beta chain MCCB/AccD1-like	Family
B, D, F, H, J B, D, F, H, J, L	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain