4LVI

MobM Relaxase Domain (MOBV; Mob_Pre) bound to plasmid pMV158 oriT DNA (22nt). Mn-bound crystal structure at pH 4.6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of a histidine-DNA nicking/joining mechanism for gene transfer and promiscuous spread of antibiotic resistance.

Pluta, R.Boer, D.R.Lorenzo-Diaz, F.Russi, S.Gomez, H.Fernandez-Lopez, C.Perez-Luque, R.Orozco, M.Espinosa, M.Coll, M.

(2017) Proc. Natl. Acad. Sci. U.S.A. 114: E6526-E6535

  • DOI: 10.1073/pnas.1702971114
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resis ...

    Relaxases are metal-dependent nucleases that break and join DNA for the initiation and completion of conjugative bacterial gene transfer. Conjugation is the main process through which antibiotic resistance spreads among bacteria, with multidrug-resistant staphylococci and streptococci infections posing major threats to human health. The MOB V family of relaxases accounts for approximately 85% of all relaxases found in Staphylococcus aureus isolates. Here, we present six structures of the MOB V relaxase MobM from the promiscuous plasmid pMV158 in complex with several origin of transfer DNA fragments. A combined structural, biochemical, and computational approach reveals that MobM follows a previously uncharacterized histidine/metal-dependent DNA processing mechanism, which involves the formation of a covalent phosphoramidate histidine-DNA adduct for cell-to-cell transfer. We discuss how the chemical features of the high-energy phosphorus-nitrogen bond shape the dominant position of MOB V histidine relaxases among small promiscuous plasmids and their preference toward Gram-positive bacteria.


    Organizational Affiliation

    Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Joint BSC-IRB Research Program in Computational Biology, Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.,Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain; miquel.coll@irbbarcelona.org.,Department of Biochemistry and Molecular Biology, University of Barcelona, 08028 Barcelona, Spain.,Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain.,Biological Research Center, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasmid recombination enzyme
A
198Streptococcus agalactiaeMutation(s): 0 
Gene Names: pre (mob)
Find proteins for P13925 (Streptococcus agalactiae)
Go to UniProtKB:  P13925
Entity ID: 2
MoleculeChainsLengthOrganism
ACTTTAT oligonucleotideB7N/A
Entity ID: 3
MoleculeChainsLengthOrganism
ATAAAGTATAGTGTG oligonucleotideC15N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 111.060α = 90.00
b = 111.060β = 90.00
c = 90.740γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
PHASERphasing
SCALAdata scaling
BESTdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Database references