3ZXQ

CRYSTAL STRUCTURE OF THE ATP-BINDING DOMAIN OF MYCOBACTERIUM TUBERCULOSIS DOST


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Activation of ATP Binding for the Autophosphorylation of Doss, a Mycobacterium Tuberculosis Histidine Kinase Lacking an ATP-Lid Motif.

Cho, H.Y.Lee, Y.H.Bae, Y.S.Kim, E.Kang, B.S.

(2013) J Biol Chem 288: 12437

  • DOI: 10.1074/jbc.M112.442467
  • Primary Citation of Related Structures:  
    3ZXO, 3ZXQ

  • PubMed Abstract: 
  • The sensor histidine kinases of Mycobacterium tuberculosis, DosS and DosT, are responsible for sensing hypoxic conditions and consist of sensor and kinase cores responsible for accepting signals and phosphorylation activity, respectively. The kinase ...

    The sensor histidine kinases of Mycobacterium tuberculosis, DosS and DosT, are responsible for sensing hypoxic conditions and consist of sensor and kinase cores responsible for accepting signals and phosphorylation activity, respectively. The kinase core contains a dimerization and histidine phosphate-accepting (DHp) domain and an ATP binding domain (ABD). The 13 histidine kinase genes of M. tuberculosis can be grouped based on the presence or absence of the ATP lid motif and F box (elements known to play roles in ATP binding) in their ABDs; DosS and DosT have ABDs lacking both these elements, and the crystal structures of their ABDs indicated that they were unsuitable for ATP binding, as a short loop covers the putative ATP binding site. Although the ABD alone cannot bind ATP, the kinase core is functional in autophosphorylation. Appropriate spatial arrangement of the ABD and DHp domain within the kinase core is required for both autophosphorylation and ATP binding. An ionic interaction between Arg(440) in the DHp domain and Glu(537) in the short loop of the ABD is available and may open the ATP binding site, by repositioning the short loop away from the site. Mutations at Arg(440) and Glu(537) reduce autophosphorylation activity. Unlike other histidine kinases containing an ATP lid, which protects bound ATP, DosS is unable to accept ATP until the ABD is properly positioned relative to the histidine; this may prevent unexpected ATP reactions. ATP binding can, therefore, function as a control mechanism for histidine kinase activity.


    Related Citations: 
    • A Gaf Domain in the Hypoxia/No-Inducible Mycobacterium Tuberculosis Doss Protein Binds Haem.
      Sardiwal, S., Kendall, S.L., Movahedzadeh, F., Rison, S.C.G., Stoker, N.G., Djordjevic, S.
      (2005) J Mol Biol 353: 929

    Organizational Affiliation

    School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, South Korea.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYPOXIA SENSOR HISTIDINE KINASE RESPONSE REGULATOR DOSTAB124Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: dosTRv2027c
EC: 2.7.13.3
Find proteins for P9WGK1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGK1 
Go to UniProtKB:  P9WGK1
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.914α = 90
b = 65.867β = 90
c = 72.704γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2012-10-03
    Changes: Derived calculations
  • Version 1.2: 2013-03-27
    Changes: Database references
  • Version 1.3: 2013-05-22
    Changes: Database references