6O8O | pdb_00006o8o

Crystal Structure of C9S disulfide state of Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulatus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.229 (Depositor) 
  • R-Value Observed: 
    0.231 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6O8O

This is version 1.4 of the entry. See complete history

Literature

Structural basis for persulfide-sensing specificity in a transcriptional regulator.

Capdevila, D.A.Walsh, B.J.C.Zhang, Y.Dietrich, C.Gonzalez-Gutierrez, G.Giedroc, D.P.

(2021) Nat Chem Biol 17: 65-70

  • DOI: https://doi.org/10.1038/s41589-020-00671-9
  • Primary Citation Related Structures: 
    6O8K, 6O8L, 6O8M, 6O8N, 6O8O

  • PubMed Abstract: 

    Cysteine thiol-based transcriptional regulators orchestrate the coordinated regulation of redox homeostasis and other cellular processes by 'sensing' or detecting a specific redox-active molecule, which in turn activates the transcription of a specific detoxification pathway. The extent to which these sensors are truly specific in cells for a singular class of reactive small-molecule stressors, for example, reactive oxygen or sulfur species, is largely unknown. Here, we report structural and mechanistic insights into the thiol-based transcriptional repressor SqrR, which reacts exclusively with oxidized sulfur species such as persulfides, to yield a tetrasulfide bridge that inhibits DNA operator-promoter binding. Evaluation of crystallographic structures of SqrR in various derivatized states, coupled with the results of a mass spectrometry-based kinetic profiling strategy, suggest that persulfide selectivity is determined by structural frustration of the disulfide form. These findings led to the identification of an uncharacterized repressor from the bacterial pathogen Acinetobacter baumannii as a persulfide sensor.


  • Organizational Affiliation
    • Department of Chemistry and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN, USA.

Macromolecule Content 

  • Total Structure Weight: 51.03 kDa 
  • Atom Count: 3,236 
  • Modeled Residue Count: 400 
  • Deposited Residue Count: 444 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcriptional regulator, ArsR family
A, B, C, D
111Rhodobacter capsulatusMutation(s): 1 
UniProt
Find proteins for D5AT91 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003))
Explore D5AT91 
Go to UniProtKB:  D5AT91
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5AT91
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
H [auth B]
I [auth B]
J [auth C]
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth C],
K [auth C],
L [auth C],
M [auth C],
O [auth D],
P [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
N [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.229 (Depositor) 
  • R-Value Observed: 0.231 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.6α = 90
b = 92.6β = 90
c = 148.98γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118157

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2020-11-11
    Changes: Database references
  • Version 1.3: 2020-12-30
    Changes: Database references
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Structure summary