1H0M

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
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	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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
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)
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	GerE	e1h0mA1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, LuxR-like	F: GerE	ECOD (1.6)
A	Autoind_bind	e1h0mA2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: Autoind_bind	ECOD (1.6)
B	GerE	e1h0mB1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, LuxR-like	F: GerE	ECOD (1.6)
B	Autoind_bind	e1h0mB2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: Autoind_bind	ECOD (1.6)
C	GerE	e1h0mC1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, LuxR-like	F: GerE	ECOD (1.6)
C	Autoind_bind	e1h0mC2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: Autoind_bind	ECOD (1.6)
D	GerE	e1h0mD1	A: alpha arrays	X: HTH	H: HTH	T: tetra-helical, LuxR-like	F: GerE	ECOD (1.6)
D	Autoind_bind	e1h0mD2	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: Autoind_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03472	Autoinducer binding domain (Autoind_bind)	Autoinducer binding domain	This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 20 ...	This domain is found a a large family of transcriptional regulators. This domain specifically binds to autoinducer molecules (N-Acyl homoserine lactones, chlorolactone and rosmarinic acid) (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).	Domain
A, B, C, D	PF00196	Bacterial regulatory proteins, luxR family (GerE)	Bacterial regulatory proteins, luxR family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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 organic cyclic compound 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
E, F, G, H	5'-D(APTPGPTPGPCPAPGPAPTP CPTPGPCPAPCPAPT)-3'	-	-	-

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.