Crystal structure of VvPlpA G389N from Vibrio vulnificus

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

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This is version 1.3 of the entry. See complete history


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

  • 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. 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

    Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thermolabile hemolysin
A, B, C
424Vibrio vulnificusMutation(s): 1 
Gene Names: CRN61_10355
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on P6G

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
K [auth C]
C12 H26 O7
Query on 1PS

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
L [auth C],
M [auth C]
C8 H11 N O3 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.946α = 90
b = 64.551β = 116.55
c = 160.649γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

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
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary