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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 ...

    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; Structural Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA. Electronic address: roland.riek@phys.chem.ethz.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inner membrane protein YgaPA127Escherichia 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D 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

View Full Validation Report



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