3D6Y | pdb_00003d6y

Crystal structure of R275E mutant of BMRR bound to DNA and berberine

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 [auth A]	d3d6ya1	All alpha proteins	Putative DNA-binding domain	Putative DNA-binding domain	DNA-binding N-terminal domain of transcription activators	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B [auth A]	d3d6ya2	Alpha and beta proteins (a+b)	Probable bacterial effector-binding domain	Probable bacterial effector-binding domain	Multidrug-binding domain of transcription activator BmrR	automated matches	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth A]	SCOP2B Superfamily	Dimerization domain of Mer-like transcriptional regulators	8093204	3002692	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Putative DNA-binding domain	8038782	3000158	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Probable bacterial effector-binding domain	8038783	3000062	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 [auth A]	MerR-DNA-bind, MerR_1	e3d6yA1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: MerR-DNA-bind, MerR_1	ECOD (develop294)
B [auth A]	FGE-sulfatase	e3d6yA2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: FGE-sulfatase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth A]	1.10.1660.10	Mainly Alpha	Orthogonal Bundle	Multidrug-efflux Transporter Regulator	Chain: A	CATH (4.3.0)
B [auth A]	1.20.5.490	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Single helix bin	CATH (4.3.0)
B [auth A]	3.20.80.10	Alpha Beta	Alpha-Beta Barrel	Multidrug-efflux Transporter 1 Regulator Bmrr	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A]	PF06445	GyrI-like small molecule binding domain (GyrI-like)	GyrI-like small molecule binding domain	This family contains the small molecule binding domain of a number of different bacterial transcription activators [1]. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecu ...	This family contains the small molecule binding domain of a number of different bacterial transcription activators [1]. This family also contains DNA gyrase inhibitors. The GyrI superfamily contains a diad of the SHS2 module, adapted for small-molecule binding [3]. The GyrI superfamily includes a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira [3].	Domain
B [auth A]	PF00376	MerR family regulatory protein (MerR)	MerR family regulatory protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth A]	Multidrug-efflux transporter 1 regulator	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	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 cellular process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process	-
A [auth B]	BMR promoter DNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A]	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily
B [auth A]	IPR047057	MerR transcriptional regulator	Family
B [auth A]	IPR011256	Regulatory factor, effector binding domain superfamily	Homologous Superfamily
B [auth A]	IPR029442	GyrI-like small molecule binding domain	Domain
B [auth A]	IPR000551	MerR-type HTH 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.