6JL1

Crystal structure of VvPlpA G389D from Vibrio vulnificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 

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This is version 1.2 of the entry. See complete history


Literature

Structural analysis of aVibriophospholipase reveals an unusual Ser-His-chloride catalytic triad.

Wan, Y.Liu, C.Ma, Q.

(2019) J Biol Chem 294: 11391-11401

  • DOI: 10.1074/jbc.RA119.008280
  • Primary Citation of Related Structures:  
    6JL1, 6JL0, 6JL2, 6JKZ

  • PubMed Abstract: 
  • Phospholipases can disrupt host membranes and are important virulence factors in many pathogens. Vv PlpA is a phospholipase A 2 secreted by Vibrio vulnificus and essential for virulence. Its homologs, termed thermolabile hemolysins (TLHs), are widely distributed in Vibrio bacteria, but no structural information for this virulence factor class is available ...

    Phospholipases can disrupt host membranes and are important virulence factors in many pathogens. Vv PlpA is a phospholipase A 2 secreted by Vibrio vulnificus and essential for virulence. Its homologs, termed thermolabile hemolysins (TLHs), are widely distributed in Vibrio bacteria, but no structural information for this virulence factor class is available. Herein, we report the crystal structure of Vv PlpA to 1.4-Å resolution, revealing that Vv PlpA contains an N-terminal domain of unknown function and a C-terminal phospholipase domain and that these two domains are packed closely together. The phospholipase domain adopts a typical SGNH hydrolase fold, containing the four conserved catalytic residues Ser, Gly, Asn, and His. Interestingly, the structure also disclosed that the phospholipase domain accommodates a chloride ion near the catalytic His residue. The chloride is five-coordinated in a distorted bipyramid geometry, accepting hydrogen bonds from a water molecule and the amino groups of surrounding residues. This chloride substitutes for the most common Asp/Glu residue and forms an unusual Ser-His-chloride catalytic triad in Vv PlpA. The chloride may orient the catalytic His and stabilize the charge on its imidazole ring during catalysis. Indeed, Vv PlpA activity depended on chloride concentration, confirming the important role of chloride in catalysis. The Vv PlpA structure also revealed a large hydrophobic substrate-binding pocket that is capable of accommodating a long-chain acyl group. Our results provide the first structure of the TLH family and uncover an unusual Ser-His-chloride catalytic triad, expanding our knowledge on the biological role of chloride.


    Organizational Affiliation

    Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thermolabile hemolysinA424Vibrio vulnificusMutation(s): 1 
Gene Names: CRN61_10355
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.397α = 90
b = 54.397β = 90
c = 233.181γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-03-03 
  • Released Date: 2019-05-15 
  • Deposition Author(s): Ma, Q., Wan, Y., Liu, C.

Funding OrganizationLocationGrant Number
Other governmentChina1000 talent program
Chinese Academy of SciencesChina100 talent program

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-15
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references