4NG2 | pdb_00004ng2

Crystal structure of LasR LBD-QslA complex from Pseudomonas aeruginosa

PDB DOI: https://doi.org/10.2210/pdb4NG2/pdb

Classification: Transcription Regulator
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-11-01 Released: 2013-12-18
Deposition Author(s): Fan, H., Wu, D.H., Song, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.277 (Depositor), 0.276 (DCC)
R-Value Work:
0.231 (Depositor), 0.231 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

QsIA disrupts LasR dimerization in antiactivation of bacterial quorum sensing

Fan, H., Dong, Y., Wu, D.H., Bowler, M.W., Zhang, L., Song, H.

(2013) Proc Natl Acad Sci U S A 110: 20765-20770

PubMed: 24319092 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1073/pnas.1314415110
Primary Citation Related Structures:
4NG2

PubMed Abstract:
The human pathogen Pseudomonas aeruginosa coordinates the expression of virulence factors by using quorum sensing (QS), a signaling cascade triggered by the QS signal molecule and its receptor, a member of the LuxR family of QS transcriptional factors (LasR). The QS threshold and response in P. aeruginosa is defined by a QS LasR-specific antiactivator (QslA), which binds to LasR and prevents it from binding to its target promoter. However, how QslA binds to LasR and regulates its DNA binding activity in QS remains elusive. Here we report the crystal structure of QslA in complex with the N-terminal ligand binding domain of LasR. QsIA exists as a functional dimer to interact with the LasR ligand binding domain. Further analysis shows that QsIA binding occupies the LasR dimerization interface and consequently disrupts LasR dimerization, thereby preventing LasR from binding to its target DNA and disturbing normal QS. Our findings provide a structural model for understanding the QslA-mediated antiactivation mechanism in QS through protein-protein interaction.

Organizational Affiliation

Institute of Molecular and Cell Biology, Singapore 138673.

Macromolecule Content

Total Structure Weight: 185.89 kDa
Atom Count: 11,158
Modeled Residue Count: 1,368
Deposited Residue Count: 1,640
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional activator protein LasR	A, B, C, D	184	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lasR
UniProt
Find proteins for P25084 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P25084 Go to UniProtKB: P25084
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25084
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	E, F, G, H, I E, F, G, H, I, J, K, L	113	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: PA1244
UniProt
Find proteins for Q9I494 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I494 Go to UniProtKB: Q9I494
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I494
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OHN Query on OHN Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain M [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth A]	M [auth A], N [auth B], O [auth C], P [auth D]	N-3-OXO-DODECANOYL-L-HOMOSERINE LACTONE C₁₆ H₂₇ N O₄ PHSRRHGYXQCRPU-AWEZNQCLSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.277 (Depositor), 0.276 (DCC)
R-Value Work: 0.231 (Depositor), 0.231 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.507	α = 90
b = 185.887	β = 90
c = 56.106	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-12-18

Deposition Author(s):

Fan, H.

Wu, D.H.

Song, H.

Revision History (Full details and data files)

Version 1.0: 2013-12-18
Type: Initial release
Version 1.1: 2015-09-23
Changes: Database references
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description