5HLI | pdb_00005hli

Structure of Disulfide formed AbfR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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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 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.

Macromolecule Content 

  • Total Structure Weight: 35.5 kDa 
  • Atom Count: 2,425 
  • Modeled Residue Count: 282 
  • Deposited Residue Count: 298 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MarR family transcriptional regulator
A, B
149Staphylococcus epidermidisMutation(s): 1 
Gene Names: ADT70_02765
UniProt
Find proteins for Q5HKZ1 (Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / 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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.534α = 90
b = 51.686β = 103.73
c = 85.935γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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, Derived calculations, Refinement description
  • Version 1.3: 2024-10-23
    Changes: Structure summary