5WZE

The structure of Pseudomonas aeruginosa aminopeptidase PepP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Function Relationship of Aminopeptidase P from Pseudomonas aeruginosa.

Peng, C.T.Liu, L.Li, C.C.He, L.H.Li, T.Shen, Y.L.Gao, C.Wang, N.Y.Xia, Y.Zhu, Y.B.Song, Y.J.Lei, Q.Yu, L.T.Bao, R.

(2017) Front Microbiol 8: 2385-2385

  • DOI: https://doi.org/10.3389/fmicb.2017.02385
  • Primary Citation of Related Structures:  
    5WZE

  • PubMed Abstract: 

    PepP is a virulence-associated gene in Pseudomonas aeruginosa , making it an attractive target for anti -P. aeruginosa drug development. The encoded protein, aminopeptidases P (Pa-PepP), is a type of X-prolyl peptidase that possesses diverse biological functions. The crystal structure verified its canonical pita-bread fold and functional tetrameric assembly, and the functional studies measured the influences of different metal ions on the activity. A trimetal manganese cluster was observed at the active site, elucidating the mechanism of inhibition by metal ions. Additionally, a loop extending from the active site appeared to be important for specific large-substrate binding. Based on the structural comparison and bacterial invasion assays, we showed that this non-conserved surface loop was critical for P. aeruginosa virulence. Taken together, these findings can extend our understanding of the catalytic mechanism and virulence-related functions of Pa-PepP and provide a solid foundation for the design of specific inhibitors against pathogenic-bacterial infections.


  • Organizational Affiliation

    Pharmaceutical and Biological Engineering Department, School of Chemical Engineering, Sichuan University, Chengdu, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminopeptidase P
A, B, C, D
452Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: pepPPA5224
UniProt
Find proteins for Q9HTW6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HTW6 
Go to UniProtKB:  Q9HTW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HTW6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
P [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PRO
Query on PRO

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CA [auth C],
H [auth A],
RA [auth D],
S [auth B]
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
LA [auth D],
MA [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
IA [auth D],
JA [auth D],
KA [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA
Query on ALA

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I [auth A],
T [auth B]
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
NA [auth D],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
FA [auth C]
GA [auth C]
HA [auth C]
K [auth A]
L [auth A]
FA [auth C],
GA [auth C],
HA [auth C],
K [auth A],
L [auth A],
M [auth A],
OA [auth D],
PA [auth D],
QA [auth D],
W [auth B],
X [auth B],
Y [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
DA [auth C],
EA [auth C],
J [auth A],
U [auth B],
V [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth A],
N [auth B],
O [auth B],
Z [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.197α = 90
b = 123.432β = 90
c = 149.485γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description