5HBN

ClpC N-terminal domain with bound phospho-arginine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.602 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Arginine phosphorylation marks proteins for degradation by a Clp protease.

Trentini, D.B.Suskiewicz, M.J.Heuck, A.Kurzbauer, R.Deszcz, L.Mechtler, K.Clausen, T.

(2016) Nature 539: 48-53

  • DOI: 10.1038/nature20122

  • PubMed Abstract: 
  • Protein turnover is a tightly controlled process that is crucial for the removal of aberrant polypeptides and for cellular signalling. Whereas ubiquitin marks eukaryotic proteins for proteasomal degradation, a general tagging system for the equivalen ...

    Protein turnover is a tightly controlled process that is crucial for the removal of aberrant polypeptides and for cellular signalling. Whereas ubiquitin marks eukaryotic proteins for proteasomal degradation, a general tagging system for the equivalent bacterial Clp proteases is not known. Here we describe the targeting mechanism of the ClpC-ClpP proteolytic complex from Bacillus subtilis. Quantitative affinity proteomics using a ClpP-trapping mutant show that proteins phosphorylated on arginine residues are selectively targeted to ClpC-ClpP. In vitro reconstitution experiments demonstrate that arginine phosphorylation by the McsB kinase is required and sufficient for the degradation of substrate proteins. The docking site for phosphoarginine is located in the amino-terminal domain of the ClpC ATPase, as resolved at high resolution in a co-crystal structure. Together, our data demonstrate that phosphoarginine functions as a bona fide degradation tag for the ClpC-ClpP protease. This system, which is widely distributed across Gram-positive bacteria, is functionally analogous to the eukaryotic ubiquitin-proteasome system.


    Organizational Affiliation

    Research Institute of Molecular Pathology (IMP), Dr-Bohr-Gasse 7, 1030 Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Negative regulator of genetic competence ClpC/MecB
A
156Bacillus subtilis (strain 168)Gene Names: clpC (mecB)
Find proteins for P37571 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P37571
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
RPI
Query on RPI

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Download CCD File 
A
phospho-arginine
C6 H15 N4 O5 P
CCTIOCVIZPCTGO-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.602 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.145 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 84.600α = 90.00
b = 84.600β = 90.00
c = 29.850γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2016-10-26
    Type: Database references
  • Version 1.2: 2016-11-09
    Type: Database references