1H0M | pdb_00001h0m

Three-dimensional structure of the quorum sensing protein TraR bound to its autoinducer and to its target DNA

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	d1h0md1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	GerE-like (LuxR/UhpA family of transcriptional regulators)	Quorum-sensing transcription factor TraR, C-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
D	d1h0md2	Alpha and beta proteins (a+b)	Profilin-like	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Transcription factor TraR, N-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
C	d1h0mc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	GerE-like (LuxR/UhpA family of transcriptional regulators)	Quorum-sensing transcription factor TraR, C-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
C	d1h0mc2	Alpha and beta proteins (a+b)	Profilin-like	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Transcription factor TraR, N-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
B	d1h0mb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	GerE-like (LuxR/UhpA family of transcriptional regulators)	Quorum-sensing transcription factor TraR, C-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
B	d1h0mb2	Alpha and beta proteins (a+b)	Profilin-like	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Transcription factor TraR, N-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
A	d1h0ma1	All alpha proteins	DNA/RNA-binding 3-helical bundle	C-terminal effector domain of the bipartite response regulators	GerE-like (LuxR/UhpA family of transcriptional regulators)	Quorum-sensing transcription factor TraR, C-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)
A	d1h0ma2	Alpha and beta proteins (a+b)	Profilin-like	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	Transcription factor TraR, N-terminal domain	Agrobacterium tumefaciens (Agrobacterium tumefaciens ) [TaxId: 358 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	C-terminal effector domain of the bipartite response regulators	8041021	3001179	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	8041024	3001697	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	8041024	3001697	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	C-terminal effector domain of the bipartite response regulators	8041021	3001179	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-terminal effector domain of the bipartite response regulators	8041021	3001179	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	8041024	3001697	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pheromone-binding domain of LuxR-like quorum-sensing transcription factors	8041024	3001697	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C-terminal effector domain of the bipartite response regulators	8041021	3001179	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)
D	Phage_CII	e1h0mD1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
D	Transpeptidase	e1h0mD2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Transpeptidase	ECOD (develop294)
C	Phage_CII	e1h0mC1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
C	Transpeptidase	e1h0mC2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Transpeptidase	ECOD (develop294)
B	Phage_CII	e1h0mB1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
B	Transpeptidase	e1h0mB2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Transpeptidase	ECOD (develop294)
A	Phage_CII	e1h0mA1	A: alpha bundles	X: EGF-like	H: YozE-like	T: Ribbon-helix-helix	F: Phage_CII	ECOD (develop294)
A	Transpeptidase	e1h0mA2	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Transpeptidase	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.30.450.80	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Transcription factor LuxR-like, autoinducer-binding domain	CATH (4.3.0)
D	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)
C	3.30.450.80	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Transcription factor LuxR-like, autoinducer-binding domain	CATH (4.3.0)
C	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	3.30.450.80	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Transcription factor LuxR-like, autoinducer-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)
A	3.30.450.80	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Transcription factor LuxR-like, autoinducer-binding domain	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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E, F, G, H	5'-D(APTPGPTPGPCPAPGPAPTP CPTPGPCPAPCPAPT)-3'	-	-	-
A, B, C, D	Transcriptional activator protein TraR	transcription regulator activity DNA-binding transcription factor activity DNA-binding transcription activator activity DNA binding sequence-specific DNA binding sequence-specific double-stranded DNA binding transcription cis-regulatory region binding binding double-stranded DNA binding nucleic acid binding transcription regulatory region nucleic acid binding	regulation of biological process response to stimulus signaling quorum sensing biological regulation cell-cell signaling detection of cell density detection of biotic stimulus response to biotic stimulus cell communication detection of stimulus cellular process	protein-containing complex protein-DNA complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000792	Transcription regulator LuxR, C-terminal	Domain
A, B, C, D	IPR036693	Transcription factor LuxR-like, autoinducer-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR016032	Signal transduction response regulator, C-terminal effector	Homologous Superfamily
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR005143	Transcription factor LuxR-like, autoinducer-binding 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.