5HBL

Native rhodanese domain of YgaP prepared with 1mM DDT is S-nitrosylated


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.617 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.jmb.2016.07.010
  • Primary Citation of Related Structures:  

  • 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-nitrosylati ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inner membrane protein YgaP
A
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ygaP
Find proteins for P55734 (Escherichia coli (strain K12))
Go to UniProtKB:  P55734
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SNC
Query on SNC
A
L-PEPTIDE LINKINGC3 H6 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.617 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.203 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 43.960α = 90.00
b = 43.960β = 90.00
c = 52.329γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
AutoPROCdata scaling
autoSHARPphasing
AutoPROCdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references