3U2A

Adaptor dependent degradation of a cell-cycle regulator reveals diversity in substrate architectures


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Adaptor-dependent degradation of a cell-cycle regulator uses a unique substrate architecture.

Rood, K.L.Clark, N.E.Stoddard, P.R.Garman, S.C.Chien, P.

(2012) Structure 20: 1223-1232

  • DOI: 10.1016/j.str.2012.04.019

  • PubMed Abstract: 
  • In Caulobacter crescentus, the ClpXP protease degrades several crucial cell-cycle regulators, including the phosphodiesterase PdeA. Degradation of PdeA requires the response regulator CpdR and signals a morphological transition in concert with initia ...

    In Caulobacter crescentus, the ClpXP protease degrades several crucial cell-cycle regulators, including the phosphodiesterase PdeA. Degradation of PdeA requires the response regulator CpdR and signals a morphological transition in concert with initiation of DNA replication. Here, we report the structure of a Per-Arnt-Sim (PAS) domain of PdeA and show that it is necessary for CpdR-dependent degradation in vivo and in vitro. CpdR acts as an adaptor, tethering the amino-terminal PAS domain to ClpXP and promoting recognition of the weak carboxyl-terminal degron of PdeA, a combination that ensures processive proteolysis. We identify sites on the PAS domain needed for CpdR recognition and find that one subunit of the PdeA dimer can be delivered to ClpXP by its partner. Finally, we show that improper stabilization of PdeA in vivo alters cellular behavior. These results introduce an adaptor/substrate pair for ClpXP and reveal broad diversity in adaptor-mediated proteolysis.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GGDEF family protein
A
129Caulobacter vibrioides (strain NA1000 / CB15N)Mutation(s): 0 
Gene Names: pdeA
Find proteins for A0A0H3CDG5 (Caulobacter vibrioides (strain NA1000 / CB15N))
Go to UniProtKB:  A0A0H3CDG5
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.167 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 63.799α = 90.00
b = 41.895β = 107.52
c = 48.659γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
HKL-2000data reduction
DMphasing
SCALEPACKdata scaling
CrystalCleardata collection
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-29
    Type: Database references
  • Version 1.2: 2018-04-04
    Type: Data collection