5XQL

Crystal structure of a Pseudomonas aeruginosa transcriptional regulator

• PDB DOI: https://doi.org/10.2210/pdb5XQL/pdb

• Classification: TRANSCRIPTION
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-06-07 Released: 2017-06-28 
• Deposition Author(s): Raju, H., Sharma, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.275 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 

Literature

Crystal structure of BrlR with c-di-GMP

Raju, H., Sharma, R.

(2017) Biochem Biophys Res Commun 490: 260-264

• PubMed: 28619510 
• DOI: https://doi.org/10.1016/j.bbrc.2017.06.033
• Primary Citation of Related Structures:  
  5XQL


• PubMed Abstract: 
  

  The transcriptional regulator BrlR is a member of the MerR family of multidrug transport activators in Pseudomonas aeruginosa. Recent study indicates that BrlR is a novel 3',5'-cyclic diguanylic acid (c-di-GMP) receptor and can be activated by c-di-GMP. To gain insight into BrlR function, we determined the structure of BrlR with c-di-GMP complex structure to 2.5 Å. The structure and size exclusion chromatography (SEC) data revealed BrlR forms a tetramer and each BrlR protomer consists of three parts, DNA-binding domain, a coiled-coil region and GyrI-like domain. There are two different c-di-GMP binding sites located mainly at the DNA binding domain of each BrlR protomer and do not overlap with the GyrI-like domain. The drug-binding pocket in GyrI-like domain is much conserved indicating it can also bind flat-shaped molecules like other multidrug resistance (MDR) proteins.

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Organizational Affiliation: 

Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, 700009, West Bengal, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 34.82 kDa 
• Atom Count: 2,286 
• Modelled Residue Count: 268 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug-efflux transporter 1 regulator	A	291	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: bmrR, AO964_25340, AOY09_00728, B0B20_02615, PAERUG_E15_London_28_01_14_00871, PAERUG_P32_London_17_VIM_2_10_11_01154
UniProt
Find proteins for Q9HUT5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUT5  Go to UniProtKB:  Q9HUT5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	B [auth A], C [auth A]	9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) C20 H24 N10 O14 P2 PKFDLKSEZWEFGL-MHARETSRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.275 
• R-Value Work: 0.232 
• R-Value Observed: 0.234 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.944	α = 90
b = 135.944	β = 90
c = 95.127	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Raju, H., Sharma, R.

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 1.1: 2017-07-05
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Database references
• Version 1.3: 2024-03-27
  Changes: Data collection, Database references, Structure summary