5HBP

The crystal of rhodanese domain of YgaP treated with SNOC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

S-Nitrosylation Induces Structural and Dynamical Changes in a Rhodanese Family Protein.

Eichmann, C.Tzitzilonis, C.Nakamura, T.Kwiatkowski, W.Maslennikov, I.Choe, S.Lipton, S.A.Riek, R.

(2016) J Mol Biol 428: 3737-3751

  • DOI: https://doi.org/10.1016/j.jmb.2016.07.010
  • Primary Citation of Related Structures:  
    5HBL, 5HBO, 5HBP, 5HBQ, 5LAM, 5LAO

  • PubMed Abstract: 

    S-Nitrosylation is well established as an important post-translational regulator in protein function and signaling. However, relatively little is known about its structural and dynamical consequences. We have investigated the effects of S-nitrosylation on the rhodanese domain of the Escherichia coli integral membrane protein YgaP by NMR, X-ray crystallography, and mass spectrometry. The results show that the active cysteine in the rhodanese domain of YgaP is subjected to two competing modifications: S-nitrosylation and S-sulfhydration, which are naturally occurring in vivo. It has been observed that in addition to inhibition of the sulfur transfer activity, S-nitrosylation of the active site residue Cys63 causes an increase in slow motion and a displacement of helix 5 due to a weakening of the interaction between the active site and the helix dipole. These findings provide an example of how nitrosative stress can exert action at the atomic level.


  • Organizational Affiliation

    Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH-Hönggerberg, CH-8093 Zürich, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inner membrane protein YgaP127Escherichia coliMutation(s): 0 
Gene Names: ygaPb2668JW2643
UniProt
Find proteins for P55734 (Escherichia coli (strain K12))
Explore P55734 
Go to UniProtKB:  P55734
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55734
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
SNC
Query on SNC
A
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.872α = 90
b = 43.872β = 90
c = 52.64γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2021-09-08
    Changes: Database references, Derived calculations
  • Version 1.3: 2024-01-10
    Changes: Data collection, Refinement description