2HJ9 | pdb_00002hj9

Crystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with the periplasmic domain of LuxQ

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	d2hj9a_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Quorum-sensing signal (autoinducer-2) binding protein LuxP	(Vibrio harveyi ) [TaxId: 669 ],	SCOPe (2.08)
B	d2hj9b_	Alpha and beta proteins (a/b)	Periplasmic binding protein-like I	Periplasmic binding protein-like I	L-arabinose binding protein-like	Quorum-sensing signal (autoinducer-2) binding protein LuxP	(Vibrio harveyi ) [TaxId: 669 ],	SCOPe (2.08)
C	d2hj9c1	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	LuxQ-periplasmic domain-like	Autoinducer 2 sensor kinase/phosphatase LuxQ	(Vibrio harveyi ) [TaxId: 669 ],	SCOPe (2.08)
D	d2hj9d_	Alpha and beta proteins (a+b)	Profilin-like	Sensory domain-like	LuxQ-periplasmic domain-like	Autoinducer 2 sensor kinase/phosphatase LuxQ	(Vibrio harveyi ) [TaxId: 669 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Type 1 solute binding protein-like	8037431	3000125	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 1 solute binding protein-like	8037431	3000125	SCOP2B (2022-06-29)
C	SCOP2 Family	LuxQ-periplasmic domain-like	8020672	4002326	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Sensory domain-like	8033052	3001802	SCOP2 (2022-06-29)
D	SCOP2B Superfamily	Sensory domain-like	8033052	3001802	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	Peripla_BP_4_N_1	e2hj9A3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_N_1	ECOD (1.6)
A	Peripla_BP_4_C	e2hj9A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_C	ECOD (1.6)
B	Peripla_BP_4_N_1	e2hj9B3	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_N_1	ECOD (1.6)
B	Peripla_BP_4_C	e2hj9B2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Periplasmic binding protein-like I	F: Peripla_BP_4_C	ECOD (1.6)
C	LuxQ-periplasm	e2hj9C1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: LuxQ-periplasm	ECOD (1.6)
D	LuxQ-periplasm	e2hj9D1	A: a+b three layers	X: Profilin-like	H: sensor domains (From Topology)	T: sensor domains	F: LuxQ-periplasm	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	CATH (4.3.0)
C	3.30.450.220	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	LuxQ periplasmic domain, N-terminal subdomain	CATH (4.3.0)
C	2.20.20.100	Mainly Beta	Single Sheet	Anthopleurin-A	LuxQ periplasmic domain, C-terminal subdomain	CATH (4.3.0)
D	3.30.450.220	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	LuxQ periplasmic domain, N-terminal subdomain	CATH (4.3.0)
D	2.20.20.100	Mainly Beta	Single Sheet	Anthopleurin-A	LuxQ periplasmic domain, C-terminal subdomain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF13407	Periplasmic binding protein domain (Peripla_BP_4)	Periplasmic binding protein domain	-	Family
C, D	PF09308	LuxQ, periplasmic (LuxQ-periplasm)	LuxQ, periplasmic	Members of this family constitute the periplasmic sensor domain of the prokaryotic protein LuxQ, and assume a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Autoinducer 2-binding periplasmic protein luxP	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 transcription regulator activity DNA-binding transcription factor activity	-	cellular anatomical structure periplasmic space
C, D	Autoinducer 2 sensor kinase/phosphatase luxQ	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding phosphoric ester hydrolase activity phosphoprotein phosphatase activity catalytic activity, acting on a protein hydrolase activity, acting on ester bonds phosphatase activity hydrolase activity catalytic activity molecular sensor activity kinase activity protein kinase activity transferase activity phosphotransferase activity, nitrogenous group as acceptor phosphotransferase activity, alcohol group as acceptor protein histidine kinase activity transferase activity, transferring phosphorus-containing groups phosphorelay sensor kinase activity molecular function regulator activity molecular transducer activity histidine phosphotransfer kinase activity	-	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR025997	Periplasmic binding protein	Domain
A, B	IPR028082	Periplasmic binding protein-like I	Homologous Superfamily
C, D	IPR043056	LuxQ periplasmic domain, N-terminal subdomain	Homologous Superfamily
C, D	IPR011006	CheY-like superfamily	Homologous Superfamily
C, D	IPR004358	Signal transduction histidine kinase-related protein, C-terminal	Domain
C, D	IPR001789	Signal transduction response regulator, receiver domain	Domain
C, D	IPR036097	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily	Homologous Superfamily
C, D	IPR029151	Periplasmic sensor-like domain superfamily	Homologous Superfamily
C, D	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
C, D	IPR003661	Signal transduction histidine kinase, dimerisation/phosphoacceptor domain	Domain
C, D	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
C, D	IPR005467	Histidine kinase domain	Domain
C, D	IPR053413	Autoinducer 2 sensor kinase/phosphatase	Family
C, D	IPR015387	LuxQ, periplasmic 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.