4YOF

DosS GAFA Domain Reduced Nitric Oxide Bound Crystal Structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Distal Hydrogen-bonding Interactions in Ligand Sensing and Signaling by Mycobacterium tuberculosis DosS.

Basudhar, D.Madrona, Y.Yukl, E.T.Sivaramakrishnan, S.Nishida, C.R.Moenne-Loccoz, P.Ortiz de Montellano, P.R.

(2016) J.Biol.Chem. 291: 16100-16111

  • DOI: 10.1074/jbc.M116.724815

  • PubMed Abstract: 
  • Mycobacterium tuberculosis DosS is critical for the induction of M. tuberculosis dormancy genes in response to nitric oxide (NO), carbon monoxide (CO), or hypoxia. These environmental stimuli, which are sensed by the DosS heme group, result in autoph ...

    Mycobacterium tuberculosis DosS is critical for the induction of M. tuberculosis dormancy genes in response to nitric oxide (NO), carbon monoxide (CO), or hypoxia. These environmental stimuli, which are sensed by the DosS heme group, result in autophosphorylation of a DosS His residue, followed by phosphotransfer to an Asp residue of the response regulator DosR. To clarify the mechanism of gaseous ligand recognition and signaling, we investigated the hydrogen-bonding interactions of the iron-bound CO and NO ligands by site-directed mutagenesis of Glu-87 and His-89. Autophosphorylation assays and molecular dynamics simulations suggest that Glu-87 has an important role in ligand recognition, whereas His-89 is essential for signal transduction to the kinase domain, a process for which Arg-204 is important. Mutation of Glu-87 to Ala or Gly rendered the protein constitutively active as a kinase, but with lower autophosphorylation activity than the wild-type in the Fe(II) and the Fe(II)-CO states, whereas the E87D mutant had little kinase activity except for the Fe(II)-NO complex. The H89R mutant exhibited attenuated autophosphorylation activity, although the H89A and R204A mutants were inactive as kinases, emphasizing the importance of these residues in communication to the kinase core. Resonance Raman spectroscopy of the wild-type and H89A mutant indicates the mutation does not alter the heme coordination number, spin state, or porphyrin deformation state, but it suggests that interdomain interactions are disrupted by the mutation. Overall, these results confirm the importance of the distal hydrogen-bonding network in ligand recognition and communication to the kinase domain and reveal the sensitivity of the system to subtle differences in the binding of gaseous ligands.


    Organizational Affiliation

    From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2517 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Redox sensor histidine kinase response regulator DevS
A, B
154Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: devS (dosS)
EC: 2.7.13.3
Find proteins for P9WGK2 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WGK2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NO
Query on NO

Download SDF File 
Download CCD File 
A, B
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 33.593α = 90.00
b = 78.847β = 90.00
c = 110.645γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-03-11 
  • Released Date: 2016-03-23 
  • Deposition Author(s): Madrona, Y.

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2016-08-10
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references, Derived calculations, Refinement description