A phenylalanine clamp controls substrate specificity in the quorum-quenching metallo-γ-lactonase from Bacillus thuringiensis.

TitleA phenylalanine clamp controls substrate specificity in the quorum-quenching metallo-γ-lactonase from Bacillus thuringiensis.
Publication TypeJournal Article
Year of Publication2013
AuthorsLiu CFeng, Liu D, Momb J, Thomas PW, Lajoie A, Petsko GA, Fast W, Ringe D
JournalBiochemistry
Volume52
Issue9
Pagination1603-10
Date Published2013 Mar 5
ISSN1520-4995
KeywordsAmidohydrolases, Bacillus thuringiensis, Crystallography, X-Ray, Homoserine, Kinetics, Models, Molecular, Mutagenesis, Site-Directed, Phenylalanine, Point Mutation, Protein Conformation, Quorum Sensing, Substrate Specificity
Abstract

Autoinducer inactivator A (AiiA) is a metal-dependent N-acyl homoserine lactone hydrolase that displays broad substrate specificity but shows a preference for substrates with long N-acyl substitutions. Previously, crystal structures of AiiA in complex with the ring-opened product N-hexanoyl-l-homoserine revealed binding interactions near the metal center but did not identify a binding pocket for the N-acyl chains of longer substrates. Here we report the crystal structure of an AiiA mutant, F107W, determined in the presence and absence of N-decanoyl-l-homoserine. F107 is located in a hydrophobic cavity adjacent to the previously identified ligand binding pocket, and the F107W mutation results in the formation of an unexpected interaction with the ring-opened product. Notably, the structure reveals a previously unidentified hydrophobic binding pocket for the substrate's N-acyl chain. Two aromatic residues, F64 and F68, form a hydrophobic clamp, centered around the seventh carbon in the product-bound structure's decanoyl chain, making an interaction that would also be available for longer substrates, but not for shorter substrates. Steady-state kinetics using substrates of various lengths with AiiA bearing mutations at the hydrophobic clamp, including insertion of a redox-sensitive cysteine pair, confirms the importance of this hydrophobic feature for substrate preference. Identifying the specificity determinants of AiiA will aid the development of more selective quorum-quenching enzymes as tools and as potential therapeutics.

DOI10.1021/bi400050j
Alternate JournalBiochemistry
PubMed ID23387521
PubMed Central IDPMC3603367
Grant ListGM26788 / GM / NIGMS NIH HHS / United States
R01 GM026788 / GM / NIGMS NIH HHS / United States