8B7F

Nuclease from C. glutamicum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The MksG nuclease is the executing part of the bacterial plasmid defense system MksBEFG.

Weiss, M.Giacomelli, G.Assaya, M.B.Grundt, F.Haouz, A.Peng, F.Petrella, S.Wehenkel, A.M.Bramkamp, M.

(2023) Nucleic Acids Res 51: 3288-3306

  • DOI: https://doi.org/10.1093/nar/gkad130
  • Primary Citation of Related Structures:  
    8B7F

  • PubMed Abstract: 

    Cells are continuously facing the risk of taking up foreign DNA that can compromise genomic integrity. Therefore, bacteria are in a constant arms race with mobile genetic elements such as phages, transposons and plasmids. They have developed several active strategies against invading DNA molecules that can be seen as a bacterial 'innate immune system'. Here, we investigated the molecular arrangement of the Corynebacterium glutamicum MksBEFG complex, which is homologous to the MukBEF condensin system. We show here that MksG is a nuclease that degrades plasmid DNA. The crystal structure of MksG revealed a dimeric assembly through its C-terminal domain that is homologous to the TOPRIM domain of the topoisomerase II family of enzymes and contains the corresponding ion binding site essential for DNA cleavage in topoisomerases. The MksBEF subunits exhibit an ATPase cycle in vitro and we reason that this reaction cycle, in combination with the nuclease activity provided by MksG, allows for processive degradation of invading plasmids. Super-resolution localization microscopy revealed that the Mks system is spatially regulated via the polar scaffold protein DivIVA. Introduction of plasmids results in an increase in DNA bound MksG, indicating an activation of the system in vivo.


  • Organizational Affiliation

    Institute for General Microbiology, Christian-Albrechts-University Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3,MksG
A, B
474Corynebacterium glutamicum ATCC 13032Mutation(s): 1 
Gene Names: SMT3YDR510WD9719.15Cgl2803
UniProt
Find proteins for Q12306 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12306 
Go to UniProtKB:  Q12306
Find proteins for Q8NLY3 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025))
Explore Q8NLY3 
Go to UniProtKB:  Q8NLY3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ12306Q8NLY3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.60 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.086α = 90
b = 126.776β = 90
c = 150.111γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Pasteur InstituteFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references, Refinement description