8AC7

Structure of Pseudomonas aeruginosa aminopeptidase, PaAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An anti-biofilm cyclic peptide targets a secreted aminopeptidase from P. aeruginosa.

Harding, C.J.Bischoff, M.Bergkessel, M.Czekster, C.M.

(2023) Nat Chem Biol 19: 1158-1166

  • DOI: https://doi.org/10.1038/s41589-023-01373-8
  • Primary Citation of Related Structures:  
    8AC7, 8AC9, 8ACG, 8ACK, 8ACR

  • PubMed Abstract: 

    Pseudomonas aeruginosa is an opportunistic pathogen that causes serious illness, especially in immunocompromised individuals. P. aeruginosa forms biofilms that contribute to growth and persistence in a wide range of environments. Here we investigated the aminopeptidase, P. aeruginosa aminopeptidase (PaAP) from P. aeruginosa, which is highly abundant in the biofilm matrix. PaAP is associated with biofilm development and contributes to nutrient recycling. We confirmed that post-translational processing was required for activation and PaAP is a promiscuous aminopeptidase acting on unstructured regions of peptides and proteins. Crystal structures of wild-type enzymes and variants revealed the mechanism of autoinhibition, whereby the C-terminal propeptide locks the protease-associated domain and the catalytic peptidase domain into a self-inhibited conformation. Inspired by this, we designed a highly potent small cyclic-peptide inhibitor that recapitulates the deleterious phenotype observed with a PaAP deletion variant in biofilm assays and present a path toward targeting secreted proteins in a biofilm context.


  • Organizational Affiliation

    Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Keratinase KP1A [auth B],
B [auth A]
510Pseudomonas aeruginosaMutation(s): 0 
UniProt
Find proteins for Q02PA2 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore Q02PA2 
Go to UniProtKB:  Q02PA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02PA2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
F [auth B]
Q [auth A]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA
Query on IPA

Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
P [auth B]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
J [auth B]
K [auth B]
L [auth B]
M [auth B]
N [auth B]
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Y [auth A],
Z [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
CA [auth A]
DA [auth A]
G [auth B]
H [auth B]
I [auth B]
CA [auth A],
DA [auth A],
G [auth B],
H [auth B],
I [auth B],
U [auth A],
V [auth A],
W [auth A],
X [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.157 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.952α = 90
b = 85.953β = 93.56
c = 98.216γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-12
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description