5HLH

Crystal structure of the overoxidized AbfR bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into the Redox-Sensing Mechanism of MarR-Type Regulator AbfR.

Liu, G.Liu, X.Xu, H.Liu, X.Zhou, H.Huang, Z.Gan, J.Chen, H.Lan, L.Yang, C.G.

(2017) J. Am. Chem. Soc. 139: 1598-1608

  • DOI: 10.1021/jacs.6b11438
  • Primary Citation of Related Structures:  5HLG, 5HLI

  • PubMed Abstract: 
  • As a master redox-sensing MarR-family transcriptional regulator, AbfR participates in oxidative stress responses and virulence regulations in Staphylococcus epidermidis. Here, we present structural insights into the DNA-binding mechanism of AbfR in d ...

    As a master redox-sensing MarR-family transcriptional regulator, AbfR participates in oxidative stress responses and virulence regulations in Staphylococcus epidermidis. Here, we present structural insights into the DNA-binding mechanism of AbfR in different oxidation states by determining the X-ray crystal structures of a reduced-AbfR/DNA complex, an overoxidized (Cys13-SO2H and Cys13-SO3H) AbfR/DNA, and 2-disulfide cross-linked AbfR dimer. Together with biochemical analyses, our results suggest that the redox regulation of AbfR-sensing displays two novel features: (i) the reversible disulfide modification, but not the irreversible overoxidation, significantly abolishes the DNA-binding ability of the AbfR repressor; (ii) either 1-disulfide cross-linked or 2-disulfide cross-linked AbfR dimer is biologically significant. The overoxidized species of AbfR, resembling the reduced AbfR in conformation and retaining the DNA-binding ability, does not exist in biologically significant concentrations, however. The 1-disulfide cross-linked modification endows AbfR with significantly weakened capability for DNA-binding. The 2-disulfide cross-linked AbfR adopts a very "open" conformation that is incompatible with DNA-binding. Overall, the concise oxidation chemistry of the redox-active cysteine allows AbfR to sense and respond to oxidative stress correctly and efficiently.


    Organizational Affiliation

    Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MarR family transcriptional regulator
A, B, C, D, E, F, G, H
147Staphylococcus epidermidis (strain ATCC 35984 / RP62A)N/A
Find proteins for Q5HKZ1 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Go to UniProtKB:  Q5HKZ1
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*AP*CP*TP*CP*AP*AP*TP*CP*GP*CP*GP*CP*GP*CP*GP*AP*TP*TP*GP*AP*GP*T)-3')I,J,K,L,M,N,O,P24synthetic construct
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 150.305α = 90.00
b = 290.914β = 90.00
c = 52.351γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Database references