5NV8

Structural basis for EarP-mediated arginine glycosylation of translation elongation factor EF-P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.294 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.289 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Basis for EarP-Mediated Arginine Glycosylation of Translation Elongation Factor EF-P.

Krafczyk, R.Macosek, J.Jagtap, P.K.A.Gast, D.Wunder, S.Mitra, P.Jha, A.K.Rohr, J.Hoffmann-Roder, A.Jung, K.Hennig, J.Lassak, J.

(2017) MBio 8: --

  • DOI: 10.1128/mBio.01412-17

  • PubMed Abstract: 
  • Glycosylation is a universal strategy to posttranslationally modify proteins. The recently discovered arginine rhamnosylation activates the polyproline-specific bacterial translation elongation factor EF-P. EF-P is rhamnosylated on arginine 32 by the ...

    Glycosylation is a universal strategy to posttranslationally modify proteins. The recently discovered arginine rhamnosylation activates the polyproline-specific bacterial translation elongation factor EF-P. EF-P is rhamnosylated on arginine 32 by the glycosyltransferase EarP. However, the enzymatic mechanism remains elusive. In the present study, we solved the crystal structure of EarP from Pseudomonas putida The enzyme is composed of two opposing domains with Rossmann folds, thus constituting a B pattern-type glycosyltransferase (GT-B). While dTDP-β-l-rhamnose is located within a highly conserved pocket of the C-domain, EarP recognizes the KOW-like N-domain of EF-P. Based on our data, we propose a structural model for arginine glycosylation by EarP. As EarP is essential for pathogenicity in P. aeruginosa, our study provides the basis for targeted inhibitor design.IMPORTANCE The structural and biochemical characterization of the EF-P-specific rhamnosyltransferase EarP not only provides the first molecular insights into arginine glycosylation but also lays the basis for targeted-inhibitor design against Pseudomonas aeruginosa infection.


    Organizational Affiliation

    Center for integrated Protein Science Munich (CiPSM), Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EF-P arginine 32 rhamnosyl-transferase
A
390Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)Mutation(s): 0 
Gene Names: earP
Find proteins for Q88LS1 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440))
Go to UniProtKB:  Q88LS1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRH
Query on TRH

Download SDF File 
Download CCD File 
A
2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
C16 H26 N2 O15 P2
ZOSQFDVXNQFKBY-CGAXJHMRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.294 Å
  • R-Value Free: 0.339 
  • R-Value Work: 0.289 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 131.680α = 90.00
b = 131.680β = 90.00
c = 46.240γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
CRANK2phasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-11
    Type: Database references
  • Version 1.2: 2017-10-18
    Type: Structure summary