2MN2

3D structure of YmoB, a modulator of biofilm formation


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An oxygen-sensitive toxin-antitoxin system.

Marimon, O.Teixeira, J.M.Cordeiro, T.N.Soo, V.W.Wood, T.L.Mayzel, M.Amata, I.Garcia, J.Morera, A.Gay, M.Vilaseca, M.Orekhov, V.Y.Wood, T.K.Pons, M.

(2016) Nat Commun 7: 13634-13634

  • DOI: https://doi.org/10.1038/ncomms13634
  • Primary Citation of Related Structures:  
    2MN2

  • PubMed Abstract: 

    The Hha and TomB proteins from Escherichia coli form an oxygen-dependent toxin-antitoxin (TA) system. Here we show that YmoB, the Yersinia orthologue of TomB, and its single cysteine variant [C117S]YmoB can replace TomB as antitoxins in E. coli. In contrast to other TA systems, [C117S]YmoB transiently interacts with Hha (rather than forming a stable complex) and enhances the spontaneous oxidation of the Hha conserved cysteine residue to a -SO x H-containing species (sulfenic, sulfinic or sulfonic acid), which destabilizes the toxin. The nuclear magnetic resonance structure of [C117S]YmoB and the homology model of TomB show that the two proteins form a four-helix bundle with a conserved buried cysteine connected to the exterior by a channel with a diameter comparable to that of an oxygen molecule. The Hha interaction site is located on the opposite side of the helix bundle.


  • Organizational Affiliation

    Biomolecular NMR Laboratory, Organic Chemistry Section, Inorganic and Organic Chemistry Department, University of Barcelona, Baldiri Reixac 10-12, Barcelona 08028, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
YmoB133Yersinia enterocoliticaMutation(s): 1 
Gene Names: ybaJYEW_DG13760ymoB
UniProt
Find proteins for A0A0E1NKQ3 (Yersinia enterocolitica)
Explore A0A0E1NKQ3 
Go to UniProtKB:  A0A0E1NKQ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0E1NKQ3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Other