1HXD

CRYSTAL STRUCTURE OF E. COLI BIOTIN REPRESSOR WITH BOUND BIOTIN

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)
B	d1hxdb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Biotin repressor-like	Biotin repressor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1hxdb2	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	Biotin repressor (BirA)	Biotin repressor/biotin holoenzyme synthetase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1hxdb3	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Biotin holoenzyme synthetase	Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1hxda1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	Biotin repressor-like	Biotin repressor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1hxda2	All beta proteins	SH3-like barrel	C-terminal domain of transcriptional repressors	Biotin repressor (BirA)	Biotin repressor/biotin holoenzyme synthetase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1hxda3	Alpha and beta proteins (a+b)	Class II aaRS and biotin synthetases	Class II aaRS and biotin synthetases	Biotin holoenzyme synthetase	Biotin repressor/biotin holoenzyme synthetase, catalytic (central) domain	(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)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8002576	3000058	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8002573	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Transcriptional regulator domain	8002578	3000121	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Transcriptional regulator domain	8002578	3000121	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8002573	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8002576	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	e1hxdB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BPL_C	ECOD (1.6)
B	HTH_11	e1hxdB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HTH_11	ECOD (1.6)
B	BPL_LplA_LipB	e1hxdB3	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	e1hxdA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: BPL_C	ECOD (1.6)
A	HTH_11	e1hxdA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: HTH_11	ECOD (1.6)
A	BPL_LplA_LipB	e1hxdA3	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	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	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)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08279	HTH domain (HTH_11)	HTH domain	This family includes helix-turn-helix domains in a wide variety of proteins.	Domain
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 prot ...	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	BIRA BIFUNCTIONAL PROTEIN	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 DNA binding nucleic acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding double-stranded DNA binding transcription regulatory region nucleic acid binding catalytic activity, acting on a protein biotin--[biotin carboxyl-carrier protein] ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity biotin binding amide binding organic acid binding vitamin binding carboxylic acid binding monocarboxylic acid binding sulfur compound binding	regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of cellular process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process macromolecule modification protein metabolic process protein modification process biotin metabolic process oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process vitamin metabolic process small molecule metabolic process sulfur compound metabolic process amide metabolic process monocarboxylic acid metabolic process water-soluble vitamin metabolic process water-soluble vitamin biosynthetic process monocarboxylic acid biosynthetic process small molecule biosynthetic process vitamin biosynthetic process amide biosynthetic process organic acid biosynthetic process biotin biosynthetic process carboxylic acid biosynthetic process sulfur compound biosynthetic process	protein-containing complex transcription regulator complex transcription repressor complex 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	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR008988	Transcriptional repressor, C-terminal	Homologous Superfamily
A, B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR004143	Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain	Domain
A, B	IPR013196	Helix-turn-helix, type 11	Domain
A, B	IPR030855	Bifunctional ligase/repressor BirA	Family
A, B	IPR003142	Biotin protein ligase, C-terminal	Domain
A, B	IPR004409	Biotin operon repressor, helix-turn-helix domain	Domain

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.