5UKY | pdb_00005uky

DHp domain of PhoR of M. tuberculosis - native data


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 
    0.217 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Asymmetric Structure of the Dimerization Domain of PhoR, a Sensor Kinase Important for the Virulence of Mycobacterium tuberculosis.

Xing, D.Ryndak, M.B.Wang, L.Kolesnikova, I.Smith, I.Wang, S.

(2017) ACS Omega 2: 3509-3517

  • DOI: https://doi.org/10.1021/acsomega.7b00612
  • Primary Citation Related Structures: 
    5UKV, 5UKY

  • PubMed Abstract: 

    The PhoP-PhoR two-component system is essential for the virulence of Mycobacterium tuberculosis ( Mtb ) and therefore represents a potential target for developing novel antituberculosis therapies. However, little is known about the mechanism by which this two-component system regulates the virulence. In this study, we demonstrated that a phoR mutant Mtb strain has phenotypes similar to those of a phoP mutant, suggesting that PhoP and PhoR work in the same pathway to regulate Mtb virulence. We determined the structure of the dimerization and histidine phosphotransfer (DHp) domain of PhoR to a 1.9 Å resolution. The structure revealed that the DHp domain is a dimer. Each subunit consists of two antiparallel α helices connected by a loop of five residues. The two subunits of the dimer fold into a four-helical bundle with a continuous hydrophobic core. The topology of the four-helical bundle is identical to the histidine kinases that are known to have a cis-autophosphorylation mechanism, suggesting that PhoR is likely to autophosphorylate in cis. The dimer is asymmetric, with one subunit having a greater bending angle than the other at the highly conserved proline residue five-residues downstream of the phosphorylation site histidine. This structural asymmetry of the dimer suggests the flexibility of the PhoR DHp domain, which is likely to be important for the signal transduction mechanism in controlling the autophosphorylation and phosphotransfer reactions and communicating with the upstream structure.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, Maryland 20814, United States.

Macromolecule Content 

  • Total Structure Weight: 17.39 kDa 
  • Atom Count: 1,235 
  • Modeled Residue Count: 148 
  • Deposited Residue Count: 148 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-binding protein
A, B
74Mycobacterium tuberculosisMutation(s): 1 
EC: 2.7.13.3
UniProt
Find proteins for P71815 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P71815 
Go to UniProtKB:  P71815
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP71815
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4

Query on PG4



Download:Ideal Coordinates CCD File
E [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A],
H [auth A],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
C [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free:  0.217 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.25α = 90
b = 74.534β = 96.64
c = 44.539γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2017-12-06 
  • Deposition Author(s): Wang, S.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079185

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description