5X80

CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS MARR FAMILY PROTEIN RV2887 COMPLEX WITH SALICYLIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5HSN - determined by Gao, Y.R., Li, D.F., Wang, D.C., Bi, L.J.  

Literature

Structural analysis of the regulatory mechanism of MarR protein Rv2887 in M. tuberculosis

Gao, Y.R.Li, D.F.Fleming, J.Zhou, Y.F.Liu, Y.Deng, J.Y.Zhou, L.Zhou, J.Zhu, G.F.Zhang, X.E.Wang, D.C.Bi, L.J.

(2017) Sci Rep 7: 6471-6471

  • DOI: 10.1038/s41598-017-01705-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • MarR family proteins are transcriptional regulators that control expression of bacterial proteins involved in metabolism, virulence, stress responses and multi-drug resistance, mainly via ligand-mediated attenuation of DNA binding. Greater understand ...

    MarR family proteins are transcriptional regulators that control expression of bacterial proteins involved in metabolism, virulence, stress responses and multi-drug resistance, mainly via ligand-mediated attenuation of DNA binding. Greater understanding of their underlying regulatory mechanism may open up new avenues for the effective treatment of bacterial infections. To gain molecular insight into the mechanism of Rv2887, a MarR family protein in M. tuberculosis, we first showed that it binds salicylate (SA) and para-aminosalicylic acid (PAS), its structural analogue and an antitubercular drug, in a 1:1 stoichiometry with high affinity. Subsequent determination and analysis of Rv2887 crystal structures in apo form, and in complex with SA, PAS and DNA showed that SA and PAS bind to Rv2887 at similar sites, and that Rv2887 interacts with DNA mainly by insertion of helix α4 into the major groove. Ligand binding triggers rotation of the wHTH domain of Rv2887 toward the dimerization domain, causing changes in protein conformation such that it can no longer bind to a 27 bp recognition sequence in the upstream region of gene Rv0560c. The structures provided here lay a foundation for the design of small molecules that target Rv2887, a potential new approach for the development of anti-mycobacterials.


    Organizational Affiliation

    Key Laboratory of RNA Biology & National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, 200237, China.,Guangdong Province Key Laboratory of TB Systems Biology and Translational Medicine, Foshan, 528000, China. blj@ibp.ac.cn.,University of the Chinese Academy of Sciences, Beijing, 100049, China.,Key Laboratory of RNA Biology & National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. blj@ibp.ac.cn.,State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.,Center for Tuberculosis Control of Guangdong Province, Guangzhou, 510630, China.,School of Stomatology and Medicine, Foshan University, Foshan, 528000, Guangdong Province, China. blj@ibp.ac.cn.,Key Laboratory of RNA Biology & National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. dcwang@ibp.ac.cn.,School of Stomatology and Medicine, Foshan University, Foshan, 528000, Guangdong Province, China.,The 4th Peoples' Hospital, Foshan, 528000, Guangdong Province, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized HTH-type transcriptional regulator Rv2887
A, B, C, D
160Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Find proteins for P9WME9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WME9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SAL
Query on SAL

Download SDF File 
Download CCD File 
A, B, C, D
2-HYDROXYBENZOIC ACID
SALICYLIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SALKa: 24500 M-1 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 57.970α = 90.00
b = 44.150β = 90.42
c = 122.160γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release