The quorum-quenching N-acyl homoserine lactone acylase PvdQ is an Ntn-hydrolase with an unusual substrate-binding pocket.
In many Gram-negative pathogens, their virulent behavior is regulated by quorum sensing, in which diffusible signals such as N-acyl homoserine lactones (AHLs) act as chemical messaging compounds. Enzymatic degradation of these diffusible signals by, e.g., lactonases or amidohydrolases abolishes AHL regulated virulence, a process known as quorum quenching. Here we report the first crystal structure of an AHL amidohydrolase, the AHL acylase PvdQ from Pseudomonas aeruginosa. PvdQ has a typical alpha/beta heterodimeric Ntn-hydrolase fold, similar to penicillin G acylase and cephalosporin acylase. However, it has a distinct, unusually large, hydrophobic binding pocket, ideally suited to recognize C12 fatty acid-like chains of AHLs. Binding of a C12 fatty acid or a 3-oxo-C12 fatty acid induces subtle conformational changes to accommodate the aliphatic chain. Furthermore, the structure of a covalent ester intermediate identifies Serbeta1 as the nucleophile and Asnbeta269 and Valbeta70 as the oxyanion hole residues in the AHL degradation process. Our structures show the versatility of the Ntn-hydrolase scaffold and can serve as a structural paradigm for Ntn-hydrolases with similar substrate preference. Finally, the quorum-quenching capabilities of PvdQ may be utilized to suppress the quorum-sensing machinery of pathogens.
Bokhove
Marcel
M
Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
Nadal Jimenez
Pol
P
Quax
Wim J
WJ
Dijkstra
Bauke W
BW
D016960:Agrobacterium tumefaciens / Q000201:enzymology; D000581:Amidohydrolases / Q000737:chemistry* / Q000378:metabolism*; D001413:Bacillus thuringiensis / Q000201:enzymology; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D020134:Catalytic Domain; D017124:Conserved Sequence; D004220:Disulfides / Q000032:analysis; D006090:Gram-Negative Bacteria / Q000201:enzymology*; D006868:Hydrolysis; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D053038:Quorum Sensing
D001426:Bacterial Proteins; D004220:Disulfides; D008024:Ligands; D000581:Amidohydrolases; C531311:N-acylhomoserine lactone-acylase, Shewanella