6O8M

Crystal Structure of C9S apo Sulfide-responsive transcriptional repressor (SqrR) from Rhodobacter capsulated bound to diamide (tetramethylazodicarboxamide).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

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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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator, ArsR family111Rhodobacter 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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LSY (Subject of Investigation/LOI)
Query on LSY

Download Ideal Coordinates CCD File 
B [auth A]N~1~,N~1~,N~2~,N~2~-tetramethylhydrazine-1,2-dicarboxamide
C6 H14 N4 O2
RAUKYARZDOSMOO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.509α = 90
b = 46.509β = 90
c = 158.468γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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: 2023-10-11
    Changes: Data collection, Database references, Refinement description