2BNW

Structural basis for cooperative binding of Ribbon-Helix-Helix Omega repressor to direct DNA heptad repeats

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	d2bnwa_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	Omega transcriptional repressor	automated matches	STREPTOCOCCUS (Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
B	d2bnwb2	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	Omega transcriptional repressor	automated matches	STREPTOCOCCUS (Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
B	d2bnwb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	STREPTOCOCCUS (Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
C	d2bnwc2	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	Omega transcriptional repressor	automated matches	STREPTOCOCCUS (Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
C	d2bnwc3	Artifacts	Tags	Tags	Tags	N-terminal Tags	STREPTOCOCCUS (Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)
D	d2bnwd_	All alpha proteins	Ribbon-helix-helix	Ribbon-helix-helix	Omega transcriptional repressor	automated matches	STREPTOCOCCUS (Streptococcus pyogenes ) [TaxId: 1314 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribbon-helix-helix	8036722	3000295	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribbon-helix-helix	8036722	3000295	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribbon-helix-helix	8036722	3000295	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribbon-helix-helix	8036722	3000295	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	Omega_Repress	e2bnwA1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Omega_Repress	ECOD (1.6)
B	Omega_Repress	e2bnwB1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Omega_Repress	ECOD (1.6)
C	Omega_Repress	e2bnwC1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Omega_Repress	ECOD (1.6)
D	Omega_Repress	e2bnwD1	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: Omega_Repress	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
B	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
C	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)
D	1.10.1220.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant	Met repressor-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF07764	Omega Transcriptional Repressor (Omega_Repress)	Omega Transcriptional Repressor	The omega transcriptional repressor regulates expression of involved in copy number control and stable maintenance of plasmids. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding ...	The omega transcriptional repressor regulates expression of involved in copy number control and stable maintenance of plasmids. The omega protein belongs to the structural superfamily of MetJ/Arc repressors featuring a ribbon-helix-helix DNA-binding motif with the beta-ribbon located in and recognising the major groove of operator DNA [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	ORF OMEGA	-	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	-
E, G	5'-D(GPAPAPTPCPAPCPAPAPAP TPCPAPCPAPAPGPC)-3'	-	-	-
F, H	5'-D(CPTPTPGPTPGPAPTPTPTP GPTPGPAPTPTPCPG)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
A, B, C, D	IPR010985	Ribbon-helix-helix	Homologous Superfamily
A, B, C, D	IPR011686	Omega transcriptional repressor	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.