3Q5F

Crystal structure of the Salmonella transcriptional regulator SlyA in complex with DNA

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	d3q5fa_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	MarR-like transcriptional regulators	Transcriptional regulator SlyA	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
B	d3q5fb_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	MarR-like transcriptional regulators	Transcriptional regulator SlyA	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8054302	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8054302	3000034	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	MarR	e3q5fA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: MarR	ECOD (1.6)
B	MarR	e3q5fB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: MarR	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01047	MarR family (MarR)	MarR family	The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is ...	The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds [1]. The structure of MarR is known [2] and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Transcriptional regulator slyA	DNA binding binding organic cyclic compound binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity	response to stimulus response to stress 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 response to stimulus response to stress 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	cellular anatomical structure intracellular anatomical structure cytoplasm
C	DNA (5'-D(APAPTPAPAPCPTPTPAPGPCPAPAPGPCPTPAPAPTPTPAPTP*A)-3')	-	-	-
D	DNA (5'-D(TPTPAPTPAPAPTPTPAPGPCPTPTPGPCPTPAPAPGPTPTPAP*T)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000835	MarR-type HTH domain	Domain
A, B	IPR023071	Transcriptional regulator, SlyA	Family
A, B	IPR023187	Transcriptional regulator MarR-type, conserved site	Conserved Site
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR039422	Transcription regulators MarR/SlyA-like	Family
A, B	IPR036390	Winged helix DNA-binding domain superfamily	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.