7M1M | pdb_00007m1m

Crystal structure of Pseudomonas aeruginosa ClpP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7M1M

This is version 1.2 of the entry. See complete history

Literature

ClpP1P2 peptidase activity promotes biofilm formation in Pseudomonas aeruginosa.

Mawla, G.D.Hall, B.M.Carcamo-Oyarce, G.Grant, R.A.Zhang, J.J.Kardon, J.R.Ribbeck, K.Sauer, R.T.Baker, T.A.

(2021) Mol Microbiol 115: 1094-1109

  • DOI: https://doi.org/10.1111/mmi.14649
  • Primary Citation Related Structures: 
    7M1L, 7M1M

  • PubMed Abstract: 

    Caseinolytic proteases (Clp) are central to bacterial proteolysis and control cellular physiology and stress responses. They are composed of a double-ring compartmentalized peptidase (ClpP) and a AAA+ unfoldase (ClpX or ClpA/ClpC). Unlike many bacteria, the opportunistic pathogen Pseudomonas aeruginosa contains two ClpP homologs: ClpP1 and ClpP2. The specific functions of these homologs, however, are largely elusive. Here, we report that the active form of PaClpP2 is a part of a heteromeric PaClpP1 7 P2 7 tetradecamer that is required for proper biofilm development. PaClpP1 14 and PaClpP1 7 P2 7 complexes exhibit distinct peptide cleavage specificities and interact differentially with P. aeruginosa ClpX and ClpA. Crystal structures reveal that PaClpP2 has non-canonical features in its N- and C-terminal regions that explain its poor interaction with unfoldases. However, experiments in vivo indicate that the PaClpP2 peptidase active site uniquely contributes to biofilm development. These data strongly suggest that the specificity of different classes of ClpP peptidase subunits contributes to the biological outcome of proteolysis. This specialized role of PaClpP2 highlights it as an attractive target for developing antimicrobial agents that interfere specifically with late-stage P. aeruginosa development.


  • Organizational Affiliation
    • Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

Macromolecule Content 

  • Total Structure Weight: 325.45 kDa 
  • Atom Count: 20,143 
  • Modeled Residue Count: 2,554 
  • Deposited Residue Count: 2,940 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
210Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
EC: 3.4.21.92
UniProt
Find proteins for Q9I2U1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I2U1 
Go to UniProtKB:  Q9I2U1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I2U1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD

Query on MPD



Download:Ideal Coordinates CCD File
AA [auth J]
BA [auth K]
CA [auth L]
DA [auth M]
EA [auth M]
AA [auth J],
BA [auth K],
CA [auth L],
DA [auth M],
EA [auth M],
FA [auth N],
O [auth A],
P [auth B],
Q [auth B],
R [auth C],
S [auth C],
T [auth D],
U [auth E],
V [auth F],
W [auth G],
X [auth H],
Y [auth I],
Z [auth J]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.250 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.975α = 66.99
b = 97.118β = 85.93
c = 108.347γ = 77.17
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata reduction

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI016892

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-06-30
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description