2DXU | pdb_00002dxu

Crystal Structure Of Biotin Protein Ligase From Pyrococcus Horikoshii Complexed with Biotinyl-5'-AMP, Mutation R48A

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	d2dxua2	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	Biotin repressor (BirA)	Biotin--[acetyl-CoA-carboxylase] ligase C-terminal domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
A	d2dxua1	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Biotin holoenzyme synthetase	Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d2dxub2	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	Biotin repressor (BirA)	Biotin--[acetyl-CoA-carboxylase] ligase C-terminal domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)
B	d2dxub1	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Biotin holoenzyme synthetase	Biotin--[acetyl-CoA-carboxylase] ligase catalytic domain	(Pyrococcus horikoshii ) [TaxId: 53953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Transcriptional regulator domain	8039898	3000121	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8039899	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8039899	3000058	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	BPL_C	e2dxuA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BPL_C	ECOD (1.6)
A	BPL_LplA_LipB	e2dxuA2	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: BPL_LplA_LipB	ECOD (1.6)
B	BPL_C	e2dxuB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BPL_C	ECOD (1.6)
B	BPL_LplA_LipB	e2dxuB1	A: a+b three layers	X: Class II aaRS and biotin synthetases (From Topology)	H: Class II aaRS and biotin synthetases (From Topology)	T: Class II aaRS and biotin synthetases	F: BPL_LplA_LipB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF03099	Biotin/lipoate A/B protein ligase family (BPL_LplA_LipB)	Biotin/lipoate A/B protein ligase family	This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin prote ...	This family includes biotin protein ligase, lipoate-protein ligase A and B. Biotin is covalently attached at the active site of certain enzymes that transfer carbon dioxide from bicarbonate to organic acids to form cellular metabolites. Biotin protein ligase (BPL) is the enzyme responsible for attaching biotin to a specific lysine at the active site of biotin enzymes. Each organism probably has only one BPL. Biotin attachment is a two step reaction that results in the formation of an amide linkage between the carboxyl group of biotin and the epsilon-amino group of the modified lysine [2]. Lipoate-protein ligase A (LPLA) catalyses the formation of an amide linkage between lipoic acid and a specific lysine residue in lipoate dependent enzymes [3]. The unusual biosynthesis pathway of lipoic acid is mechanistically intertwined with attachment of the cofactor [5].	Domain
A, B	PF02237	Biotin protein ligase C terminal domain (BPL_C)	Biotin protein ligase C terminal domain	The function of this structural domain is unknown. It is found to the C terminus of the biotin protein ligase catalytic domain Pfam:PF01317.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	biotin--[acetyl-CoA-carboxylase] ligase	catalytic activity, acting on a protein biotin--[biotin carboxyl-carrier protein] ligase 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 catalytic activity, acting on a protein biotin--[biotin carboxyl-carrier protein] ligase 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 cation binding metal ion binding	macromolecule modification metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process protein modification process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004408	Biotin--acetyl-CoA-carboxylase ligase	Family
A, B	IPR004143	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain	Domain
A, B	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR003142	Biotin protein ligase, C-terminal	Domain
A, B	IPR008988	Transcriptional repressor, C-terminal	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.