2DTH | pdb_00002dth

The Crystal Structure of the Orthorhombic Form of Biotin Protein Ligase From Pyrococcus Horikoshii OT3 in Complex with Biotin and ADP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B	d2dthb1	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 OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
B	d2dthb2	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 OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d2dtha1	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 OT3 ) [TaxId: 70601 ],	SCOPe (2.08)
A	d2dtha2	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 OT3 ) [TaxId: 70601 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Transcriptional regulator domain	8039898	3000121	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8039899	3000058	SCOP2B (2022-06-29)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	BPL_C	e2dthB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BPL_C	ECOD (1.6)
B	BPL_LplA_LipB	e2dthB2	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)
A	BPL_C	e2dthA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BPL_C	ECOD (1.6)
A	BPL_LplA_LipB	e2dthA2	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)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	235aa long hypothetical 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	-	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.