3JZI

Crystal structure of biotin carboxylase from E. Coli in complex with benzimidazole series

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3jzia3	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Biotin carboxylase (BC), C-domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3jzia1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Biotin carboxylase (BC), N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3jzia2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Biotin carboxylase (BC), domain 2	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3jzib3	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Biotin carboxylase (BC), C-domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3jzib1	Alpha and beta proteins (a/b)	PreATP-grasp domain	PreATP-grasp domain	BC N-terminal domain-like	Biotin carboxylase (BC), N-terminal domain	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3jzib2	Alpha and beta proteins (a+b)	ATP-grasp	Glutathione synthetase ATP-binding domain-like	BC ATP-binding domain-like	Biotin carboxylase (BC), domain 2	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3jzib4	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	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	8034650	3000094	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PreATP-grasp domain	8034649	3001680	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Rudiment single hybrid motif	8034648	3001910	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutathione synthetase ATP-binding domain-like	8034650	3000094	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PreATP-grasp domain	8034649	3001680	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Rudiment single hybrid motif	8034648	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)
A	ATP-grasp	e3jziA1	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	e3jziA2	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_carb_N	e3jziA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	ECOD (1.6)
B	ATP-grasp	e3jziB1	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	e3jziB2	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_carb_N	e3jziB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: PreATP-grasp domain	F: Biotin_carb_N	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	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
A	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	3.40.50.20	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.30.470.20	Alpha Beta	2-Layer Sandwich	D-amino Acid Aminotransferase	Chain A, domain 1	CATH (4.3.0)
B	3.30.1490.20	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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 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	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	Biotin carboxylase	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 acetyl-CoA carboxylase activity ligase activity, forming carbon-carbon bonds catalytic activity ligase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity biotin carboxylase activity ligase activity, forming carbon-nitrogen bonds cation binding metal ion binding	fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular 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 organic substance metabolic process biosynthetic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process cellular biosynthetic process cellular 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 organic substance metabolic process biosynthetic process organic substance biosynthetic process cellular lipid metabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process lipid 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 cellular nitrogen compound biosynthetic process nucleobase-containing compound metabolic process ribonucleotide biosynthetic process heterocycle metabolic process malonyl-CoA biosynthetic process phosphate-containing compound metabolic process sulfur compound metabolic process thioester metabolic process phosphorus metabolic process ribose phosphate biosynthetic process nucleoside phosphate metabolic process cellular nitrogen compound metabolic process amide biosynthetic process nucleotide metabolic process organic cyclic compound metabolic process sulfur compound biosynthetic process aromatic compound biosynthetic process organophosphate biosynthetic process organic cyclic compound biosynthetic process nucleoside phosphate biosynthetic 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 purine nucleotide metabolic process acyl-CoA metabolic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process nitrogen compound metabolic 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 heterocycle biosynthetic process purine-containing compound metabolic process organophosphate metabolic process cellular aromatic compound metabolic process regulation of cellular process negative regulation of small molecule metabolic process regulation of lipid metabolic process negative regulation of biological process negative regulation of lipid biosynthetic process negative regulation of cellular metabolic process regulation of primary metabolic process cellular ketone metabolic process regulation of small molecule metabolic process regulation of biological process regulation of cellular ketone metabolic process negative regulation of metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process regulation of metabolic process negative regulation of lipid metabolic process negative regulation of cellular process negative regulation of fatty acid biosynthetic process regulation of biosynthetic process negative regulation of fatty acid metabolic process biological regulation regulation of cellular biosynthetic process negative regulation of biosynthetic process regulation of lipid biosynthetic process	acetyl-CoA carboxylase complex protein-containing complex intracellular anatomical structure catalytic complex cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR005481	Biotin carboxylase-like, N-terminal domain	Domain
A, B	IPR011761	ATP-grasp fold	Domain
A, B	IPR011764	Biotin carboxylation domain	Domain
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR004549	Acetyl-CoA carboxylase, biotin carboxylase	Family
A, B	IPR005482	Biotin carboxylase, C-terminal	Domain
A, B	IPR005479	Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain	Domain
A, B	IPR016185	Pre-ATP-grasp domain superfamily	Homologous Superfamily
A, B	IPR011054	Rudiment single hybrid motif	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.