3U2A | pdb_00003u2a

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

• PDB DOI: https://doi.org/10.2210/pdb3U2A/pdb

• Classification: HYDROLASE
• Organism(s): Caulobacter vibrioides
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-10-02 Released: 2012-05-30 
• Deposition Author(s): Rood, K., Clark, N.E., Garman, S.C., Chien, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

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

• PubMed: 22682744 
• DOI: https://doi.org/10.1016/j.str.2012.04.019
• Primary Citation Related Structures: 
  3U2A


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.98 kDa 
• Atom Count: 1,037 
• Modeled Residue Count: 112 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GGDEF family protein	A	129	Caulobacter vibrioides	Mutation(s): 0  Gene Names: CC3396(PdeA), CC_3396 EC: 3.1.4.52
UniProt
Find proteins for A0A0H3CDG5 (Caulobacter vibrioides (strain NA1000 / CB15N)) Explore A0A0H3CDG5  Go to UniProtKB:  A0A0H3CDG5

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.206 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.799	α = 90
b = 41.895	β = 107.52
c = 48.659	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Rood, K., Clark, N.E., Garman, S.C., Chien, P.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-08-29
  Changes: Database references
• Version 1.2: 2018-04-04
  Changes: Data collection
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary