6JL1

Crystal structure of VvPlpA G389D from Vibrio vulnificus

Summary for 6JL1

• Entry DOI: 10.2210/pdb6jl1/pdb
• Descriptor: Thermolabile hemolysin (2 entities in total)
• Functional Keywords: vibrio, phospholipase, sgnh hydrolase, hydrolase
• Biological source: Vibrio vulnificus
• Total number of polymer chains: 1
• Total formula weight: 48187.59

Authors

Ma, Q.,Wan, Y.,Liu, C. (deposition date: 2019-03-03, release date: 2019-05-15, Last modification date: 2024-11-13)

Primary citation

Wan, Y.,Liu, C.,Ma, Q.
Structural analysis of aVibriophospholipase reveals an unusual Ser-His-chloride catalytic triad.
J.Biol.Chem., 294:11391-11401, 2019

PubMed Abstract: Phospholipases can disrupt host membranes and are important virulence factors in many pathogens. PlpA is a phospholipase A secreted by and essential for virulence. Its homologs, termed thermolabile hemolysins (TLHs), are widely distributed in bacteria, but no structural information for this virulence factor class is available. Herein, we report the crystal structure of PlpA to 1.4-Å resolution, revealing that 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 PlpA. The chloride may orient the catalytic His and stabilize the charge on its imidazole ring during catalysis. Indeed, PlpA activity depended on chloride concentration, confirming the important role of chloride in catalysis. The 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.

PubMed: 31073025
DOI: 10.1074/jbc.RA119.008280

Experimental method

X-RAY DIFFRACTION (2.29 Å)