5HLH

Crystal structure of the overoxidized AbfR bound to DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1021/jacs.6b11438
  • Primary Citation of Related Structures:  
    5HLG, 5HLH, 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 different oxidation states by determining the X-ray crystal structures of a reduced-AbfR/DNA complex, an overoxidized (Cys13-SO 2 H and Cys13-SO 3 H) 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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MarR family transcriptional regulator147Staphylococcus epidermidisMutation(s): 1 
Gene Names: ADT70_02765
UniProt
Find proteins for Q5HKZ1 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Explore Q5HKZ1 
Go to UniProtKB:  Q5HKZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HKZ1
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
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')24synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
OCS
Query on OCS
I [auth A]
J [auth B]
K [auth C]
L [auth D]
M [auth E]
I [auth A],
J [auth B],
K [auth C],
L [auth D],
M [auth E],
N [auth F],
O [auth G],
P [auth H]
L-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.305α = 90
b = 290.914β = 90
c = 52.351γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-04-05
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2023-11-15
    Changes: Data collection