5WZE | pdb_00005wze

The structure of Pseudomonas aeruginosa aminopeptidase PepP

• PDB DOI: https://doi.org/10.2210/pdb5WZE/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-01-17 Released: 2018-01-17 
• Deposition Author(s): Bao, R., Peng, C.T., Liu, L., He, L.H., Li, C.C., Li, T., Shen, Y.L., Zhu, Y.B., Song, Y.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.221 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

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

• PubMed: 29259588 
• DOI: https://doi.org/10.3389/fmicb.2017.02385
• Primary Citation 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.
Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China.
School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 206.09 kDa 
• Atom Count: 15,378 
• Modeled Residue Count: 1,777 
• Deposited Residue Count: 1,808 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase P	A, B, C, D	452	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: pepP, PA5224 EC: 3.4.11.9
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

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	P [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PRO	CA [auth C], H [auth A], RA [auth D], S [auth B]	PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N
SO4	G [auth A], LA [auth D], MA [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	F [auth A], IA [auth D], JA [auth D], KA [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ALA	I [auth A], T [auth B]	ALANINE C3 H7 N O2 QNAYBMKLOCPYGJ-REOHCLBHSA-N
EDO	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	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	DA [auth C], EA [auth C], J [auth A], U [auth B], V [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	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 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.197	α = 90
b = 123.432	β = 90
c = 149.485	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Bao, R., Peng, C.T., Liu, L., He, L.H., Li, C.C., Li, T., Shen, Y.L., Zhu, Y.B., Song, Y.J.

Revision History  

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