4DKY | pdb_00004dky

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 [H37Ra]

• PDB DOI: https://doi.org/10.2210/pdb4DKY/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-05 Released: 2013-02-06 
• Deposition Author(s): Bhowmick, T., Ramagopal, U.A., Ghosh, S., Nagaraja, V., Ramakumar, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 
  0.248 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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

• PubMed: 24916461 
• DOI: https://doi.org/10.1038/ncomms5124
• Primary Citation Related Structures: 
  4DKY, 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 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.

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Organizational Affiliation: 
• 1] Department of Physics, Indian Institute of Science, Bangalore 560012, India [2].
1] Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India [2].
Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India.
1] Albert Einstein College of Medicine, Jack and Pearl Resnick Campus, 1300 Morris Park Avenue, Ullmann Building, Room 409, Bronx, New York 10461, USA [2] Biological Sciences Division, Poornaprajna Institute of Scientific Research, Bangalore 562110, India.
Department of Physics, Indian Institute of Science, Bangalore 560012, India.
1] Department of Microbiology and Cell biology, Indian Institute of Science, Bangalore 560012, India [2] Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.31 kDa 
• Atom Count: 1,550 
• Modeled Residue Count: 198 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein HU homolog	A, B	106	Mycobacterium tuberculosis H37Ra	Mutation(s): 0  Gene Names: hupB EC: 1.16.3.1
UniProt
Find proteins for A5U6Z7 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5U6Z7  Go to UniProtKB:  A5U6Z7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free:  0.248 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.115	α = 90
b = 37.052	β = 115.29
c = 64.854	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Bhowmick, T., Ramagopal, U.A., Ghosh, S., Nagaraja, V., Ramakumar, S.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2014-08-27
  Changes: Database references
• Version 1.2: 2023-07-26
  Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 1.3: 2023-11-08
  Changes: Data collection, Refinement description