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- PDB-9uxt: The Structural Basis of ClpP1 in Pseudomonas plecoglossicida -

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Basic information

Entry
Database: PDB / ID: 9uxt
TitleThe Structural Basis of ClpP1 in Pseudomonas plecoglossicida
ComponentsClp protease
KeywordsHYDROLASE / Pseudomonas plecoglossicida / caseinolytic proteases / tetradecameric / Cryo-EM structure
Function / homologyClp protease proteolytic subunit /Translocation-enhancing protein TepA / Clp protease / ClpP/crotonase-like domain superfamily / peptidase activity / proteolysis / Clp protease
Function and homology information
Biological speciesPseudomonas plecoglossicida NBRC 103162 = DSM 15088 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / Resolution: 3.07 Å
AuthorsJingjie, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: PLoS Pathog / Year: 2026
Title: Structural and mechanistic insights into caseinolytic protease inhibition for antimicrobial development against Pseudomonas plecoglossicida.
Authors: Jingjie Chen / Ping Zhang / Hongxin Guan / Bing Gong / Xiaoding Li / Zekai Li / Fan Li / Biao Zhou / Xuemin Chen / Xinhua Chen / Songying Ouyang / Yong-An Zhang /
Abstract: The caseinolytic protease (ClpP) is an emerging antibacterial target. Pseudomonas plecoglossicida (Pp), a pathogen causing visceral white spot disease in Larimichthys crocea, encodes two ClpP ...The caseinolytic protease (ClpP) is an emerging antibacterial target. Pseudomonas plecoglossicida (Pp), a pathogen causing visceral white spot disease in Larimichthys crocea, encodes two ClpP paralogs, PpClpP1 and PpClpP2. This study characterizes their distinct structural and functional properties. Phylogenetic and biochemical analysis revealed that PpClpP2 functions as a canonical serine protease with high peptidase activity, while PpClpP1 is evolutionarily divergent, exhibiting low inherent activity due to an unconventional Ser-His-Pro catalytic triad and a truncated N-terminal domain. Cryo-EM structure determination of PpClpP1 confirmed a homotetradecameric assembly with a dilated axial pore and a non-canonical catalytic geometry. In contrast, AlphaFold-predicted PpClpP2 displayed a compact structure with a canonical Ser-His-Asp triad. The subunits formed a stable heterotetradecamer (PpClpP1P2) with enhanced proteolytic activity compared to individual homotetradecameric. Pull-down assays demonstrated that PpClpP2, but not PpClpP1, specifically interacts with the unfoldase PpClpX, and the PpClpP1P2 heterotetradecamer further augmented PpClpX-mediated degradation of model substrates. Notably, the proteasome inhibitor bortezomib (BTZ) selectively inhibited PpClpP1 by binding to a unique pocket near the active site without engaging the catalytic serine, thereby suppressing bacterial growth in a PpClpP1-dependent manner. This study elucidates the structural basis of functional divergence between PpClpP paralogs, highlights their synergistic interplay in proteolysis, and identifies PpClpP1 as a druggable target for antibacterial development.
History
DepositionMay 15, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Clp protease
B: Clp protease
C: Clp protease
D: Clp protease
E: Clp protease
F: Clp protease
G: Clp protease
H: Clp protease
I: Clp protease
J: Clp protease
K: Clp protease
L: Clp protease
M: Clp protease
N: Clp protease


Theoretical massNumber of molelcules
Total (without water)285,60414
Polymers285,60414
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Clp protease


Mass: 20400.279 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas plecoglossicida NBRC 103162 = DSM 15088 (bacteria)
Gene: DVB73_02735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAD0VSB1
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: ClpP tetradecamer / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas plecoglossicida (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION9.03particle selection
9PHENIX1.19.2_4158model refinement
13RELION9.033D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39438 / Symmetry type: POINT
Atomic model buildingDetails: predicted / Source name: Other / Type: experimental model
RefinementHighest resolution: 3.07 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00320496
ELECTRON MICROSCOPYf_angle_d0.4927832
ELECTRON MICROSCOPYf_dihedral_angle_d3.842786
ELECTRON MICROSCOPYf_chiral_restr0.0383066
ELECTRON MICROSCOPYf_plane_restr0.0033598

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