4YWZ

Crystal structure of the extracellular receptor domain of the essential sensor kinase WalK from Staphylococcus aureus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and mechanism of the essential two-component signal-transduction system WalKR in Staphylococcus aureus.

Ji, Q.Chen, P.J.Qin, G.Deng, X.Hao, Z.Wawrzak, Z.Yeo, W.S.Quang, J.W.Cho, H.Luo, G.Z.Weng, X.You, Q.Luan, C.H.Yang, X.Bae, T.Yu, K.Jiang, H.He, C.

(2016) Nat Commun 7: 11000-11000

  • DOI: 10.1038/ncomms11000

  • PubMed Abstract: 
  • Most low GC Gram-positive bacteria possess an essential walKR two-component system (TCS) for signal transduction involved in regulating cell wall homoeostasis. Despite the well-established intracellular regulatory mechanism, the role of this TCS in e ...

    Most low GC Gram-positive bacteria possess an essential walKR two-component system (TCS) for signal transduction involved in regulating cell wall homoeostasis. Despite the well-established intracellular regulatory mechanism, the role of this TCS in extracellular signal recognition and factors that modulate the activity of this TCS remain largely unknown. Here we identify the extracellular receptor of the kinase 'WalK' (erWalK) as a key hub for bridging extracellular signal input and intracellular kinase activity modulation in Staphylococcus aureus. Characterization of the crystal structure of erWalK revealed a canonical Per-Arnt-Sim (PAS) domain for signal sensing. Single amino-acid mutation of potential signal-transduction residues resulted in severely impaired function of WalKR. A small molecule derived from structure-based virtual screening against erWalK is capable of selectively activating the walKR TCS. The molecular level characterization of erWalK will not only facilitate exploration of natural signal(s) but also provide a template for rational design of erWalK inhibitors.


    Organizational Affiliation

    Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sensor protein kinase WalK
A, B
152Staphylococcus aureus (strain Newman)Mutation(s): 1 
Gene Names: walK (vicK)
EC: 2.7.13.3
Find proteins for A6QD58 (Staphylococcus aureus (strain Newman))
Go to UniProtKB:  A6QD58
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.165 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 66.701α = 90.00
b = 66.701β = 90.00
c = 80.492γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
RESOLVEphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI074658

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations