5LAM

Refined 3D NMR structure of the cytoplasmic rhodanese domain of the inner membrane protein YgaP from Escherichia coli


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 2.1 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: 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 YgaP108Escherichia coli K-12Mutation(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
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesR21 NS080799
National Institutes of HealthUnited StatesP01 HD29587
National Institutes of HealthUnited StatesR01 NS086890

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-09-28
    Changes: Database references
  • Version 1.2: 2018-01-31
    Changes: Author supporting evidence
  • Version 2.0: 2019-10-23
    Changes: Atomic model, Data collection, Experimental preparation
  • Version 2.1: 2024-06-19
    Changes: Data collection, Database references