4KK4 | pdb_00004kk4

YwlE arginine phosphatase - C7S mutant with phosphorylated active site serine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.215 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1016/j.celrep.2013.05.023
  • Primary Citation of Related Structures:  
    4KK3, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Low molecular weight protein-tyrosine-phosphatase YwlE152Bacillus subtilis subsp. subtilis str. 168Mutation(s): 1 
Gene Names: ywlEBSU36930ipc-31d
EC: 3.1.3.48 (PDB Primary Data), 3.9.1.2 (UniProt)
UniProt
Find proteins for P39155 (Bacillus subtilis (strain 168))
Explore P39155 
Go to UniProtKB:  P39155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39155
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.215 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.84α = 90
b = 39.34β = 89.7
c = 40.67γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
DNAdata collection
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-03
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary