4PIC

YwlE arginine phosphatase from Geobacillus stearothermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chasing phosphoarginine proteins: development of a selective enrichment method using a phosphatase trap.

Trentini, D.B.Fuhrmann, J.Mechtler, K.Clausen, T.

(2014) Mol.Cell Proteomics --: --

  • DOI: 10.1074/mcp.O113.035790

  • PubMed Abstract: 
  • Arginine phosphorylation is an emerging post-translational protein modification implicated in the bacterial stress response. Although early reports suggested that arginine phosphorylation also occurs in higher eukaryotes, its overall prevalence was n ...

    Arginine phosphorylation is an emerging post-translational protein modification implicated in the bacterial stress response. Although early reports suggested that arginine phosphorylation also occurs in higher eukaryotes, its overall prevalence was never studied using modern mass spectrometry methods, owing to technical difficulties arising from the acid lability of phosphoarginine. As shown recently, the McsB and YwlE proteins from Bacillus subtilis function as a highly specific protein arginine kinase and phosphatase couple, shaping the phosphoarginine proteome. Using a B. subtilis ΔywlE strain as a source for arginine-phosphorylated proteins, we were able to adapt mass spectrometry (MS) protocols to the special chemical properties of the arginine modification. Despite this progress, the analysis of protein arginine phosphorylation in eukaryotes is still challenging, given the great abundance of serine/threonine phosphorylations that would compete with phosphoarginine during the phosphopeptide enrichment procedure, as well as during data-dependent MS acquisition. We thus set out to establish a method for the selective enrichment of arginine-phosphorylated proteins as an initial step in the phosphoproteomic analysis. For this purpose, we developed a substrate-trapping mutant of the YwlE phosphatase that retains binding affinity toward arginine-phosphorylated proteins but cannot hydrolyze the captured substrates. By testing a number of active site substitutions, we identified a YwlE mutant (C9A) that stably binds to arginine-phosphorylated proteins. We further improved the substrate-trapping efficiency by impeding the oligomerization of the phosphatase mutant. The engineered YwlE trap efficiently captured arginine-phosphorylated proteins from complex B. subtilis ΔywlE cell extracts, thus facilitating identification of phosphoarginine sites in the large pool of cellular protein modifications. In conclusion, we present a novel tool for the selective enrichment and subsequent MS analysis of arginine phosphorylation, which is a largely overlooked protein modification that might be important for eukaryotic cell signaling.


    Organizational Affiliation

    From the ‡Research Institute of Molecular Pathology - IMP, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginine phosphatase Ywle
A, B
156Geobacillus stearothermophilusGene Names: ywle
EC: 3.9.1.2
Find proteins for S0F332 (Geobacillus stearothermophilus)
Go to UniProtKB:  S0F332
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.434α = 90.00
b = 75.753β = 92.37
c = 47.717γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Advisory, Derived calculations, Other, Refinement description, Source and taxonomy