4YZE | pdb_00004yze

Crystal structure of E.coli NemR reduced form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.255 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.205 (Depositor) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4YZE

This is version 1.2 of the entry. See complete history

Literature

Does the Transcription Factor NemR Use a Regulatory Sulfenamide Bond to Sense Bleach?

Gray, M.J.Li, Y.Leichert, L.I.Xu, Z.Jakob, U.

(2015) Antioxid Redox Signal 23: 747-754

  • DOI: https://doi.org/10.1089/ars.2015.6346
  • Primary Citation Related Structures: 
    4YZE

  • PubMed Abstract: 

    Reactive chlorine species (RCS), such as hypochlorous acid (i.e., bleach), are antimicrobial oxidants produced by the innate immune system. Like many redox-regulated transcription factors, the Escherichia coli repressor NemR responds to RCS by using the reversible oxidation of highly conserved cysteines to alter its DNA-binding affinity. However, earlier work showed that RCS response in NemR does not depend on any commonly known oxidative cysteine modifications. We have now determined the crystal structure of NemR, showing that the regulatory cysteine, Cys106, is in close proximity to a highly conserved lysine (Lys175). We used crystallographic, biochemical, and mass spectrometric analyses to analyze the role of this lysine residue in RCS sensing. Based on our results, we hypothesize that RCS treatment of NemR results in the formation of a reversible Cys106-Lys175 sulfenamide bond. This is, to our knowledge, the first description of a protein whose function is regulated by a cysteine-lysine sulfenamide thiol switch, constituting a novel addition to the biological repertoire of functional redox switches.


  • Organizational Affiliation
    • 1 Department of Molecular, Cellular, and Developmental Biology, University of Michigan , Ann Arbor, Michigan.

Macromolecule Content 

  • Total Structure Weight: 89.47 kDa 
  • Atom Count: 5,786 
  • Modeled Residue Count: 756 
  • Deposited Residue Count: 804 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
HTH-type transcriptional repressor NemR
A, B, C, D
201Escherichia coli K-12Mutation(s): 5 
Gene Names: nemRydhMb1649JW5874
UniProt
Find proteins for P67430 (Escherichia coli (strain K12))
Explore P67430 
Go to UniProtKB:  P67430
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67430
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.255 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.205 (Depositor) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.438α = 90
b = 67.443β = 90
c = 213.864γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description