1W96

Crystal Structure of Biotin Carboxylase Domain of Acetyl-coenzyme A Carboxylase from Saccharomyces cerevisiae in Complex with Soraphen A

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1w96a1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Acetyl-CoA carboxylase, BC-C subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1w96a2	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Acetyl-CoA carboxylase, BC-N subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1w96a3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Acetyl-CoA carboxylase, BC-M subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1w96b1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Acetyl-CoA carboxylase, BC-C subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1w96b2	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Acetyl-CoA carboxylase, BC-N subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1w96b3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Acetyl-CoA carboxylase, BC-M subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1w96c1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Acetyl-CoA carboxylase, BC-C subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1w96c2	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Acetyl-CoA carboxylase, BC-N subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1w96c3	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Acetyl-CoA carboxylase, BC-M subdomain	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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	Rudiment single hybrid motif	8043358	3001910	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8043359	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rudiment single hybrid motif	8043358	3001910	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8043361	3000094	SCOP2B (2022-06-29)
C	SCOP2 Family	BC ATP-binding domain-like	8030982	4002053	SCOP2 (2022-06-29)
C	SCOP2 Family	BC N-terminal domain-like	8030980	4003858	SCOP2 (2022-06-29)
C	SCOP2 Family	BC C-terminal domain-like	8030979	4002928	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Glutathione synthetase ATP-binding domain-like	8043361	3000094	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	PreATP-grasp domain	8043359	3001680	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Rudiment single hybrid motif	8043358	3001910	SCOP2 (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	PF02786	e1w96A1	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: PF02786	ECOD (1.6)
A	PF02785	e1w96A2	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: PF02785	ECOD (1.6)
A	PF00289	e1w96A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PF00289	ECOD (1.6)
B	PF02786	e1w96B1	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: PF02786	ECOD (1.6)
B	PF02785	e1w96B2	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: PF02785	ECOD (1.6)
B	PF00289	e1w96B3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PF00289	ECOD (1.6)
C	PF02786	e1w96C1	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: PF02786	ECOD (1.6)
C	PF02785	e1w96C2	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: PF02785	ECOD (1.6)
C	PF00289	e1w96C3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: PF00289	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.90.1770.10	Alpha Beta	Alpha-Beta Complex	PreATP-grasp fold	PreATP-grasp domain	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)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.90.1770.10	Alpha Beta	Alpha-Beta Complex	PreATP-grasp fold	PreATP-grasp domain	CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
C	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.90.1770.10	Alpha Beta	Alpha-Beta Complex	PreATP-grasp fold	PreATP-grasp domain	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	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, C	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, B, C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	ACETYL-COENZYME A 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 organic cyclic compound binding anion 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 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 acetyl-CoA carboxylase activity ligase activity, forming carbon-carbon bonds identical protein binding protein binding protein homodimerization activity protein dimerization activity amide binding acyl-CoA binding acetyl-CoA binding sulfur compound binding carboxyl- or carbamoyltransferase activity transferase activity, transferring one-carbon groups transferase activity cation binding metal ion binding	nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process malonyl-CoA metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process malonyl-CoA biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process nucleoside bisphosphate metabolic process ribonucleoside bisphosphate biosynthetic process malonyl-CoA metabolic process nucleotide biosynthetic process organonitrogen compound biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process malonyl-CoA biosynthetic process phosphate-containing compound metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process thioester metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process cellular metabolic process primary metabolic process amide biosynthetic process nucleotide metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic process metabolic process purine ribonucleotide metabolic process purine nucleotide biosynthetic process ribose phosphate metabolic process purine nucleoside bisphosphate metabolic process ribonucleoside bisphosphate metabolic process thioester biosynthetic process cellular biosynthetic process purine nucleotide metabolic process organic substance metabolic process acyl-CoA metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process purine nucleoside bisphosphate biosynthetic process amide metabolic process carbohydrate derivative biosynthetic process organonitrogen compound metabolic process nucleoside bisphosphate biosynthetic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process organophosphate metabolic process cellular process protein localization establishment of protein localization cellular localization nitrogen compound transport nucleocytoplasmic transport transport nuclear transport organic substance transport intracellular transport protein localization to nucleus establishment of localization localization import into nucleus establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle establishment of localization in cell protein import into nucleus 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 cellular lipid metabolic process monocarboxylic acid metabolic process lipid metabolic process long-chain fatty acid biosynthetic process long-chain fatty acid metabolic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity 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 intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity 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, C	IPR011763	Acetyl-coenzyme A carboxyltransferase, C-terminal	Domain
A, B, C	IPR029045	ClpP/crotonase-like domain superfamily	Homologous Superfamily
A, B, C	IPR011762	Acetyl-coenzyme A carboxyltransferase, N-terminal	Domain
A, B, C	IPR049074	Acetyl-CoA carboxylase, BT domain	Domain
A, B, C	IPR011764	Biotin carboxylation domain	Domain
A, B, C	IPR034733	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta	Domain
A, B, C	IPR049076	Acetyl-CoA carboxylase	Family
A, B, C	IPR011054	Rudiment single hybrid motif	Homologous Superfamily
A, B, C	IPR013537	Acetyl-CoA carboxylase, central domain	Domain
A, B, C	IPR011053	Single hybrid motif	Homologous Superfamily
A, B, C	IPR001882	Biotin-binding site	Binding Site
A, B, C	IPR000089	Biotin/lipoyl attachment	Domain
A, B, C	IPR005481	Biotin carboxylase-like, N-terminal domain	Domain
A, B, C	IPR011761	ATP-grasp fold	Domain
A, B, C	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B, C	IPR005482	Biotin carboxylase, C-terminal	Domain
A, B, C	IPR005479	Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain	Domain
A, B, C	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.