2J9G | pdb_00002j9g

Crystal structure of Biotin carboxylase from E. coli in complex with AMPPNP and ADP

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	d2j9ga1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Biotin carboxylase (BC), C-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2j9ga2	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 ) [TaxId: 562 ],	SCOPe (2.08)
A	d2j9ga3	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 ) [TaxId: 562 ],	SCOPe (2.08)
B	d2j9gb1	All beta proteins	Barrel-sandwich hybrid	Rudiment single hybrid motif	BC C-terminal domain-like	Biotin carboxylase (BC), C-domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2j9gb2	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 ) [TaxId: 562 ],	SCOPe (2.08)
B	d2j9gb3	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 ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	BC C-terminal domain-like	8022268	4002928	SCOP2 (2022-06-29)
A	SCOP2 Family	BC N-terminal domain-like	8022269	4003858	SCOP2 (2022-06-29)
A	SCOP2 Family	BC ATP-binding domain-like	8022270	4002053	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Rudiment single hybrid motif	8034648	3001910	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PreATP-grasp domain	8034649	3001680	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Glutathione synthetase ATP-binding domain-like	8034650	3000094	SCOP2 (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		e2j9gA1	A: Protein kinase/SAICAR synthase/ATP-grasp	X: Protein kinase/SAICAR synthase/ATP-grasp	H: ATP-grasp	T: CPSase_L_D2	F:	ECOD (20:10:01)
A		e2j9gA2	A: alpha/beta-Hammerhead/Barrel-sandwich hybrid	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: CO dehydrogenase molybdoprotein N-domain-like	T: Biotin_carb_C	F:	ECOD (20:10:01)
A		e2j9gA3	A: Rossmann-like	X: Rossmann-related	H: PreATP-grasp domain	T: Biotin_carb_N	F:	ECOD (20:10:01)
B		e2j9gB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Hexapep,Acetyltransf_11	F:	ECOD (20:10:01)
B		e2j9gB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: CBAH	F:	ECOD (20:10:01)
B		e2j9gB3	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)

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 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

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 anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding 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 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 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 nucleoside phosphate metabolic process malonyl-CoA metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process organophosphate biosynthetic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process malonyl-CoA biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate biosynthetic process sulfur compound metabolic process phosphorus metabolic process regulation of cellular process negative regulation of small molecule metabolic process ketone metabolic process regulation of lipid metabolic process negative regulation of biological process negative regulation of lipid biosynthetic process regulation of primary metabolic process regulation of small molecule metabolic process negative regulation of cellular process negative regulation of fatty acid biosynthetic process regulation of biosynthetic process regulation of biological process negative regulation of fatty acid metabolic process negative regulation of metabolic process biological regulation regulation of ketone metabolic process negative regulation of biosynthetic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process regulation of lipid biosynthetic process regulation of metabolic process negative regulation of lipid metabolic process	acetyl-CoA carboxylase complex protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex cytoplasm 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	IPR051602	Acetyl-CoA Carboxylase Biotin Carboxylase Component	Family
A, B	IPR013815	ATP-grasp fold, subdomain 1	Homologous Superfamily
A, B	IPR005479	Carbamoyl phosphate synthase, ATP-binding domain	Domain
A, B	IPR004549	Acetyl-CoA carboxylase, biotin carboxylase	Family
A, B	IPR005482	Biotin carboxylase, C-terminal	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 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.