4EC6

Ntf2-like, potential transfer protein TraM from Gram-positive conjugative plasmid pIP501


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The 2.5 A Structure of the Enterococcus Conjugation Protein TraM resembles VirB8 Type IV Secretion Proteins.

Goessweiner-Mohr, N.Grumet, L.Arends, K.Pavkov-Keller, T.Gruber, C.C.Gruber, K.Birner-Gruenberger, R.Kropec-Huebner, A.Huebner, J.Grohmann, E.Keller, W.

(2013) J.Biol.Chem. 288: 2018-2028

  • DOI: 10.1074/jbc.M112.428847

  • PubMed Abstract: 
  • Conjugative plasmid transfer is the most important means of spreading antibiotic resistance and virulence genes among bacteria and therefore presents a serious threat to human health. The process requires direct cell-cell contact made possible by a m ...

    Conjugative plasmid transfer is the most important means of spreading antibiotic resistance and virulence genes among bacteria and therefore presents a serious threat to human health. The process requires direct cell-cell contact made possible by a multiprotein complex that spans cellular membranes and serves as a channel for macromolecular secretion. Thus far, well studied conjugative type IV secretion systems (T4SS) are of Gram-negative (G-) origin. Although many medically relevant pathogens (e.g., enterococci, staphylococci, and streptococci) are Gram-positive (G+), their conjugation systems have received little attention. This study provides structural information for the transfer protein TraM of the G+ broad host range Enterococcus conjugative plasmid pIP501. Immunolocalization demonstrated that the protein localizes to the cell wall. We then used opsonophagocytosis as a novel tool to verify that TraM was exposed on the cell surface. In these assays, antibodies generated to TraM recruited macrophages and enabled killing of pIP501 harboring Enteroccocus faecalis cells. The crystal structure of the C-terminal, surface-exposed domain of TraM was determined to 2.5 Å resolution. The structure, molecular dynamics, and cross-linking studies indicated that a TraM trimer acts as the biological unit. Despite the absence of sequence-based similarity, TraM unexpectedly displayed a fold similar to the T4SS VirB8 proteins from Agrobacterium tumefaciens and Brucella suis (G-) and to the transfer protein TcpC from Clostridium perfringens plasmid pCW3 (G+). Based on the alignments of secondary structure elements of VirB8-like proteins from mobile genetic elements and chromosomally encoded T4SS from G+ and G- bacteria, we propose a new classification scheme of VirB8-like proteins.


    Organizational Affiliation

    Karl-Franzens-University Graz, Institute of Molecular Biosciences, Structural Biology, 8010 Graz, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative uncharacterized protein
A, B, C, D, E, F
161Enterococcus faecalisMutation(s): 0 
Find proteins for Q8L1C7 (Enterococcus faecalis)
Go to UniProtKB:  Q8L1C7
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 39.210α = 89.91
b = 54.980β = 86.44
c = 93.470γ = 78.63
Software Package:
Software NamePurpose
SOLVEphasing
REFMACrefinement
XDSdata reduction
RESOLVEphasing
PDB_EXTRACTdata extraction
XDSdata scaling
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-01-09
    Type: Database references
  • Version 1.2: 2013-02-06
    Type: Database references