4KK3

YwlE arginine phosphatase - wildtype


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria.

Fuhrmann, J.Mierzwa, B.Trentini, D.B.Spiess, S.Lehner, A.Charpentier, E.Clausen, T.

(2013) Cell Rep 3: 1832-1839

  • DOI: 10.1016/j.celrep.2013.05.023
  • Primary Citation of Related Structures:  4KK4

  • PubMed Abstract: 
  • Many cellular pathways are regulated by the competing activity of protein kinases and phosphatases. The recent identification of arginine phosphorylation as a protein modification in bacteria prompted us to analyze the molecular basis of targeting ph ...

    Many cellular pathways are regulated by the competing activity of protein kinases and phosphatases. The recent identification of arginine phosphorylation as a protein modification in bacteria prompted us to analyze the molecular basis of targeting phospho-arginine. In this work, we characterize an annotated tyrosine phosphatase, YwlE, that counteracts the protein arginine kinase McsB. Strikingly, structural studies of YwlE reaction intermediates provide a direct view on a captured arginine residue. Together with biochemical data, the crystal structures depict the evolution of a highly specific phospho-arginine phosphatase, with the use of a size-and-polarity filter for distinguishing phosphorylated arginine from other phosphorylated side chains. To confirm the proposed mechanism, we performed bioinformatic searches for phosphatases, employing a similar selectivity filter, and identified a protein in Drosophila melanogaster exhibiting robust arginine phosphatase activity. In sum, our findings uncover the molecular framework for specific targeting of phospho-arginine and suggest that protein arginine (de)phosphorylation may be relevant in eukaryotes.


    Organizational Affiliation

    Research Institute of Molecular Pathology (IMP), A-1030 Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Low molecular weight protein-tyrosine-phosphatase YwlE
A
151Bacillus subtilis (strain 168)Gene Names: ywlE
EC: 3.9.1.2
Find proteins for P39155 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39155
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.131α = 90.00
b = 40.749β = 92.26
c = 41.056γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALAdata scaling
PHENIXrefinement
SHARPphasing
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references