3R0J

Structure of PhoP from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Response Regulator PhoP from Mycobacterium tuberculosis Reveals a Dimer through the Receiver Domain.

Menon, S.Wang, S.

(2011) Biochemistry 50: 5948-5957

  • DOI: 10.1021/bi2005575

  • PubMed Abstract: 
  • The PhoP protein from Mycobacterium tuberculosis is a response regulator of the OmpR/PhoB subfamily, whose structure consists of an N-terminal receiver domain and a C-terminal DNA-binding domain. How the DNA-binding activities are regulated by phosph ...

    The PhoP protein from Mycobacterium tuberculosis is a response regulator of the OmpR/PhoB subfamily, whose structure consists of an N-terminal receiver domain and a C-terminal DNA-binding domain. How the DNA-binding activities are regulated by phosphorylation of the receiver domain remains unclear due to a lack of structural information on the full-length proteins. Here we report the crystal structure of the full-length PhoP of M. tuberculosis. Unlike other known structures of full-length proteins of the same subfamily, PhoP forms a dimer through its receiver domain with the dimer interface involving α4-β5-α5, a common interface for activated receiver domain dimers. However, the switch residues, Thr99 and Tyr118, are in a conformation resembling those of nonactivated receiver domains. The Tyr118 side chain is involved in the dimer interface interactions. The receiver domain is tethered to the DNA-binding domain through a flexible linker and does not impose structural constraints on the DNA-binding domain. This structure suggests that phosphorylation likely facilitates/stabilizes receiver domain dimerization, bringing the DNA-binding domains to close proximity, thereby increasing their binding affinity for direct repeat DNA sequences.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP
A, B
250Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: phoP
Find proteins for P71814 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P71814
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
B
R-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-GSVOUGTGSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
MSO
Query on MSO
A, B
L-PEPTIDE LINKINGC5 H11 N O3 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 79.228α = 90.00
b = 138.242β = 90.00
c = 58.906γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data collection
PHENIXmodel building
HKL-2000data reduction
PHENIXphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-03-08 
  • Released Date: 2011-07-13 
  • Deposition Author(s): Menon, S., Wang, S.

Revision History 

  • Version 1.0: 2011-07-13
    Type: Initial release
  • Version 1.1: 2014-10-29
    Type: Structure summary