5CSL | pdb_00005csl

Crystal structure of the 500 kD yeast acetyl-CoA carboxylase holoenzyme dimer

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)
B	SCOP2B Superfamily	ClpP/crotonase	8035307	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rudiment single hybrid motif	8043358	3001910	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	ClpP/crotonase	8035309	3000033	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8043361	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8043359	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8043361	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PreATP-grasp domain	8043359	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ClpP/crotonase	8035309	3000033	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	ClpP/crotonase	8035307	3000033	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rudiment single hybrid motif	8043358	3001910	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)
B	ACC_central_1st_1	e5cslB3	A: alpha bundles	X: Bromodomain-like	H: Four-helical bundle in acetyl-CoA carboxylase (From Topology)	T: Four-helical bundle in acetyl-CoA carboxylase	F: ACC_central_1st_1	ECOD (1.6)
B	ACC_central_1st	e5cslB4	A: alpha superhelices	X: Repetitive alpha hairpins	H: Helical domain in acetyl-CoA carboxylase (From Topology)	T: Helical domain in acetyl-CoA carboxylase	F: ACC_central_1st	ECOD (1.6)
B	KOG0368	e5cslB1	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: KOG0368	ECOD (1.6)
B	ATP-grasp	e5cslB9	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)
B	Biotin_carb_C	e5cslB11	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)
B	Biotin_lipoyl	e5cslB2	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)
B	Biotin_carb_N	e5cslB10	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
B	ACC_central_2nd	e5cslB5	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Acetyl-CoA carboxylase AC4 and AC5 domains (From Topology)	T: Acetyl-CoA carboxylase AC4 and AC5 domains	F: ACC_central_2nd	ECOD (1.6)
B	Carboxyl_trans_C	e5cslB7	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)
A	ACC_central_1st_1	e5cslA5	A: alpha bundles	X: Bromodomain-like	H: Four-helical bundle in acetyl-CoA carboxylase (From Topology)	T: Four-helical bundle in acetyl-CoA carboxylase	F: ACC_central_1st_1	ECOD (1.6)
A	ACC_central_1st	e5cslA3	A: alpha superhelices	X: Repetitive alpha hairpins	H: Helical domain in acetyl-CoA carboxylase (From Topology)	T: Helical domain in acetyl-CoA carboxylase	F: ACC_central_1st	ECOD (1.6)
A	KOG0368	e5cslA6	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: KOG0368	ECOD (1.6)
A	ATP-grasp	e5cslA9	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	e5cslA11	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	e5cslA4	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	e5cslA10	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
A	ACC_central_2nd	e5cslA2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Acetyl-CoA carboxylase AC4 and AC5 domains (From Topology)	T: Acetyl-CoA carboxylase AC4 and AC5 domains	F: ACC_central_2nd	ECOD (1.6)
A	Carboxyl_trans_C	e5cslA7	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)
B	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 (utative)
B	2.40.460.10	Mainly Beta	Beta Barrel	ClpP/crotonase fold	Biotin dependent carboxylase carboxyltransferase	CATH (utative)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (utative)
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 (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF21385	Acetyl-CoA carboxylase, BT domain (ACCA_BT)	Acetyl-CoA carboxylase, BT domain	This is the BC-CT interaction domain (BT) which is between the BC (biotin carboxylase, which catalyses the MgATP-dependent carboxylation of N1' atom of biotin) and BCCP (biotin carboxyl carrier protein) domains of Acetyl-CoA carboxylase. This domain ...	This is the BC-CT interaction domain (BT) which is between the BC (biotin carboxylase, which catalyses the MgATP-dependent carboxylation of N1' atom of biotin) and BCCP (biotin carboxyl carrier protein) domains of Acetyl-CoA carboxylase. This domain helps to mediate interactions between the BC and CT (carboxyltransferase) domains [1-3].	Domain
A, B	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, B	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, B	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 in ...	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, B	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, B	PF08326	Acetyl-CoA carboxylase, central region (ACC_central)	Acetyl-CoA carboxylase, central region	-	Family
A, B	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, B	Acetyl-CoA carboxylase	biotin carboxylase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding biotin carboxylase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding CoA carboxylase activity acetyl-CoA carboxylase activity ligase activity, forming carbon-carbon bonds identical protein binding protein binding protein homodimerization activity protein dimerization activity acetyl-CoA binding amide binding acyl-CoA binding sulfur compound binding carboxyl- or carbamoyltransferase activity transferase activity, transferring one-carbon groups transferase activity cation binding metal ion binding	malonyl-CoA metabolic process thioester biosynthetic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process malonyl-CoA biosynthetic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process amide metabolic process thioester metabolic process phosphorus metabolic process malonyl-CoA metabolic process thioester biosynthetic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process malonyl-CoA biosynthetic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process amide metabolic process thioester metabolic process phosphorus metabolic process nucleoside phosphate metabolic process primary metabolic process amide biosynthetic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport establishment of localization in cell macromolecule localization protein localization to organelle protein import into nucleus intracellular protein localization intracellular protein transport acetyl-CoA metabolic process acetyl-CoA biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process carboxylic acid metabolic process lipid biosynthetic process organic acid biosynthetic process organic acid metabolic process fatty acid biosynthetic process carboxylic acid biosynthetic process monocarboxylic acid metabolic process lipid metabolic process long-chain fatty acid metabolic process long-chain fatty acid biosynthetic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cytosol organelle subcompartment membrane endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane acetyl-CoA carboxylase complex protein-containing complex catalytic complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011763	Acetyl-coenzyme A carboxyltransferase, C-terminal	Domain
A, B	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
A, B	IPR049074	Acetyl-CoA carboxylase, BT domain	Domain
A, B	IPR011764	Biotin carboxylation domain	Domain
A, B	IPR005479	Carbamoyl phosphate synthase, ATP-binding domain	Domain
A, B	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain
A, B	IPR049076	Acetyl-CoA carboxylase	Family
A, B	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
A, B	IPR013537	Acetyl-CoA carboxylase, central domain	Domain
A, B	IPR011053	Single hybrid motif	Homologous Superfamily
A, B	IPR001882	Biotin-binding site	Binding Site
A, B	IPR000089	Biotin/lipoyl attachment	Domain
A, B	IPR005481	Biotin carboxylase-like, N-terminal domain	Domain
A, B	IPR011761	ATP-grasp fold	Domain
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR005482	Biotin carboxylase, C-terminal	Domain
A, B	IPR016185	Pre-ATP-grasp domain superfamily	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.