3JSO

Classic Protein With a New Twist: crystal structure of a LexA repressor DNA complex

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	d3jsoa1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3jsoa2	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	LexA-related	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3jsob1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3jsob2	All beta proteins	LexA/Signal peptidase	LexA/Signal peptidase	LexA-related	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	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	8002596	3000034	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	LexA/Signal peptidase-like	8002599	3000103	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8002596	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	LexA/Signal peptidase-like	8002599	3000103	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	Peptidase_S24	e3jsoA1	A: beta barrels	X: SH3	H: LexA/Signal peptidase (From Topology)	T: LexA/Signal peptidase	F: Peptidase_S24	ECOD (1.6)
A	LexA_DNA_bind	e3jsoA2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: LexA_DNA_bind	ECOD (1.6)
B	Peptidase_S24	e3jsoB1	A: beta barrels	X: SH3	H: LexA/Signal peptidase (From Topology)	T: LexA/Signal peptidase	F: Peptidase_S24	ECOD (1.6)
B	LexA_DNA_bind	e3jsoB2	A: alpha arrays	X: HTH	H: HTH	T: winged	F: LexA_DNA_bind	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)
A	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	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)
B	2.10.109.10	Mainly Beta	Ribbon	Umud Fragment, subunit A	Umud Fragment, subunit A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01726	LexA DNA binding domain (LexA_DNA_bind)	LexA DNA binding domain	This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif [1]. This domain is found associated with Pfam:P ...	This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif [1]. This domain is found associated with Pfam:PF00717 the auto-proteolytic domain of LexA EC:3.4.21.88.	Domain
A, B	PF00717	Peptidase S24-like (Peptidase_S24)	Peptidase S24-like	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	DNA (5'-D(TPAPTPAPCPTPGPTPAPTPAPTPAPTPAPTPAPCPAPGPTPA)-3')	-	-	-
A, B	LexA repressor	DNA binding binding organic cyclic compound binding nucleic acid binding 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 peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity DNA binding binding organic cyclic compound binding nucleic acid binding 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 peptidase activity catalytic activity, acting on a protein serine hydrolase activity serine-type peptidase activity hydrolase activity serine-type endopeptidase activity catalytic activity endopeptidase activity identical protein binding protein binding transcription regulator activity DNA-binding transcription repressor activity DNA-binding transcription factor activity	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process regulation of cellular process negative regulation of biological process negative regulation of cellular metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription regulation of RNA metabolic process organic substance biosynthetic process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process negative regulation of DNA-templated transcription regulation of biological process cellular metabolic process negative regulation of metabolic process primary metabolic process regulation of cellular metabolic process negative regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process negative regulation of macromolecule biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleic acid biosynthetic process organic substance metabolic process negative regulation of cellular process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process biological regulation regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process negative regulation of biosynthetic process DNA replication DNA metabolic process DNA repair SOS response organonitrogen compound metabolic process proteolysis protein metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR015927	Peptidase S24/S26A/S26B/S26C	Domain
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR006199	LexA repressor, DNA-binding domain	Domain
A, B	IPR039418	LexA-like	Domain
A, B	IPR006200	Transcription regulator LexA	Family
A, B	IPR036286	LexA/Signal peptidase-like superfamily	Homologous Superfamily
A, B	IPR006197	Peptidase S24, LexA-like	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.