5Y9O

The apo structure of Legionella pneumophila WipA

• PDB DOI: https://doi.org/10.2210/pdb5Y9O/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Legionella pneumophila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-08-26 Released: 2018-05-16 
• Deposition Author(s): Xie, W., Jia, Q.
• Funding Organization(s): Fundamental Research Funds for the Central Universities, the Science and Technology Program of Guangzhou

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.282 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

Literature

Legionella pneumophila effector WipA, a bacterial PPP protein phosphatase with PTP activity

Jia, Q., Lin, Y., Gou, X., He, L., Shen, D., Chen, D., Xie, W., Lu, Y.

(2018) Acta Biochim Biophys Sin (Shanghai) 50: 547-554

• PubMed: 29701815 
• DOI: https://doi.org/10.1093/abbs/gmy042
• Primary Citation of Related Structures:  
  5Y9O


• PubMed Abstract: 
  

  The gram-negative bacterium Legionella pneumophila invades human's lung and causes Legionnaires' disease. To benefit its survival and replication in cellular milieu, L. pneumophila secrets at least 330 effector proteins into host cells. We found that the effector WipA has the protein tyrosine phosphatase (PTP) activity but does not depend on the classical CX5R motif for activity, suggesting that WipA is an unconventional PTP. Meanwhile, the presence of three other highly conserved motifs typically seen in protein serine/threonine phosphatases and the poor inhibition of WipA activity by okadaic acid led us to propose that WipA is a bacterial protein phosphatase. In addition, the determination of the 2.55-Å crystal structure of WipA revealed that WipA resembles cold-active protein tyrosine phosphatase (CAPTPase), and therefore very likely shares the same catalytic mechanism.

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Organizational Affiliation: 

School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 96.76 kDa 
• Atom Count: 6,346 
• Modelled Residue Count: 802 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WipA	A, B	412	Legionella pneumophila	Mutation(s): 0  Gene Names: wipA
UniProt
Find proteins for Q5GA16 (Legionella pneumophila) Explore Q5GA16  Go to UniProtKB:  Q5GA16

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 0.282 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.608	α = 90
b = 95.976	β = 90
c = 106.635	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Xie, W., Jia, Q.

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Funding Organization	Location	Grant Number
Fundamental Research Funds for the Central Universities	China	16lgjc76
the Science and Technology Program of Guangzhou	China	201504010025
the Science and Technology Program of Guangzhou	China	201605030012

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description