4DKY

Crystal structure Analysis of N terminal region containing the dimerization domain and DNA binding domain of HU protein(Histone like protein-DNA binding) from Mycobacterium tuberculosis [H37Rv]


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.478 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Targeting Mycobacterium tuberculosis nucleoid-associated protein HU with structure-based inhibitors

Bhowmick, T.Ghosh, S.Dixit, K.Ganesan, V.Ramagopal, U.A.Dey, D.Sarma, S.P.Ramakumar, S.Nagaraja, V.

(2014) Nat Commun 5: 4124-4124

  • DOI: 10.1038/ncomms5124
  • Primary Citation of Related Structures:  4PT4

  • PubMed Abstract: 
  • The nucleoid-associated protein HU plays an important role in maintenance of chromosomal architecture and in global regulation of DNA transactions in bacteria. Although HU is essential for growth in Mycobacterium tuberculosis (Mtb), there have been n ...

    The nucleoid-associated protein HU plays an important role in maintenance of chromosomal architecture and in global regulation of DNA transactions in bacteria. Although HU is essential for growth in Mycobacterium tuberculosis (Mtb), there have been no reported attempts to perturb HU function with small molecules. Here we report the crystal structure of the N-terminal domain of HU from Mtb. We identify a core region within the HU-DNA interface that can be targeted using stilbene derivatives. These small molecules specifically inhibit HU-DNA binding, disrupt nucleoid architecture and reduce Mtb growth. The stilbene inhibitors induce gene expression changes in Mtb that resemble those induced by HU deficiency. Our results indicate that HU is a potential target for the development of therapies against tuberculosis.


    Organizational Affiliation

    1] Department of Physics, Indian Institute of Science, Bangalore 560012, India [2].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-binding protein HU homolog
A, B
106Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: hup (hlp, hupB, lbp21)
Find proteins for P9WMK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WMK7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.478 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.183 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 55.115α = 90.00
b = 37.052β = 115.29
c = 64.854γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CBASSdata collection
PHASERphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2014-08-27
    Type: Database references