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 1.1 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: 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 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YmoBA133Yersinia enterocoliticaMutation(s): 1 
Gene Names: ybaJYEW_DG13760ymoBtomBERS137941_00299
UniProt
Find proteins for A0A0E1NKQ3 (Yersinia enterocolitica)
Explore A0A0E1NKQ3 
Go to UniProtKB:  A0A0E1NKQ3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2MN2 Olderado

Structure Validation

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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