8R3N | pdb_00008r3n

Crystal structure of PfpI, Pseudomonas aeruginosa PAO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 
    0.282 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Pseudomonas aeruginosa PfpI is a methylglyoxalase.

Grimm, L.Wijaya, A.Askenasy, I.Nazeer, R.R.Seki, H.Brear, P.D.Figueroa, W.Spring, D.R.Welch, M.

(2025) J Biological Chem 301: 108374-108374

  • DOI: https://doi.org/10.1016/j.jbc.2025.108374
  • Primary Citation of Related Structures:  
    8R3N

  • PubMed Abstract: 

    Pseudomonas aeruginosa is an opportunistic pathogen, commonly associated with human airway infections. Based on its amino acid sequence similarity with Pyrococcus furiosusprotease I, P. aeruginosa PfpI was originally annotated as an intracellular protease. In this work, we show that PfpI is a methylglyoxalase. The X-ray crystal structure of the purified protein was solved to 1.4 Å resolution. The structural data indicated that PfpI shares the same constellation of active site residues (including the catalytic Cys112 and His113) as those seen in a well-characterized bacterial methylglyoxalase from Escherichia coli, YhbO. Using NMR, we confirmed that PfpI qualitatively converted methylglyoxal into lactic acid. Quantitation of lactate produced by the methylglyoxalase activity of PfpI yielded a k cat of 102 min -1 and a K M of 369 μM. Mutation of Cys112 and His113 in PfpI led to complete loss of methylglyoxalase activity. To investigate the functional impact of PfpI in vivo, a ΔpfpI deletion mutant was made. Quantitative proteomic analyses revealed a pattern of changes consistent with perturbation of ribosomal function, Zn 2+ limitation, C1 metabolism, and glutathione metabolism. These findings are consistent with PfpI being a glutathione-independent methylglyoxalase. Previously, transposon insertion (pfpI::Tn) mutants have been reported to exhibit phenotypes associated with antibiotic resistance, motility and the response to oxidative stress. However, the ΔpfpI mutant generated in this study displayed none of these phenotypes. Whole-genome sequencing of the previously described pfpI::Tn mutants revealed that they also contain a variety of other genetic changes that likely account for their observed phenotypes.


  • Organizational Affiliation
    • Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease PfpIA [auth B],
B [auth X]
179Pseudomonas aeruginosaMutation(s): 0 
Gene Names: pfpI
UniProt
Find proteins for Q9I6D8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I6D8 
Go to UniProtKB:  Q9I6D8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I6D8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free:  0.282 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.99α = 90
b = 78.71β = 90
c = 103.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United Kingdom--
Jardine FoundationHong Kong--
Rosetrees TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Database references