9B2J

Structure of the quorum quenching lactonase GcL I237M mutant

Summary for 9B2J

• Entry DOI: 10.2210/pdb9b2j/pdb
• Related: 6N9Q 6N9R 6n9i 9AYT 9B2I
• Descriptor: quorum-quenching N-acyl-homoserine lactonase, SULFATE ION, COBALT (II) ION, ... (7 entities in total)
• Functional Keywords: quorum sensing, quorum quenching, lactonase, metalloenzyme, hydrolase
• Biological source: Parageobacillus caldoxylosilyticus
• Total number of polymer chains: 3
• Total formula weight: 105454.66

Authors

Corbella, M.,Bravo, J.A.,Demkiv, A.O.,Calixto, A.R.,Sompiyachoke, K.,Bergonzi, C.,Kamerlin, S.C.L.,Elias, M. (deposition date: 2024-03-15, release date: 2024-11-06)

Primary citation

Corbella, M.,Bravo, J.,Demkiv, A.O.,Calixto, A.R.,Sompiyachoke, K.,Bergonzi, C.,Brownless, A.R.,Elias, M.H.,Kamerlin, S.C.L.
Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases.
Jacs Au, 4:3519-3536, 2024

PubMed Abstract: Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade acyl L-homoserine lactones (AHLs). They play a role in a microbial communication system known as quorum sensing, which contributes to pathogenicity and biofilm formation. Designing quorum quenching () enzymes that can interfere with this communication allows them to be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific communication signals requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of GcL, which is a highly proficient and thermostable MLL with broad substrate specificity. We show that GcL not only accepts a broad range of substrates but also hydrolyzes these substrates through at least two different mechanisms. Further, the preferred mechanism appears to depend on both the substrate structure and/or the nature of the residues lining the active site. We demonstrate that other lactonases, such as AiiA and AaL, show similar mechanistic promiscuity, suggesting that this is a shared feature among MLLs. Mechanistic promiscuity has been seen previously in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and protein engineering perspective: in addition to optimizing for specific substrates, it may be possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes but also of other mechanistically promiscuous enzymes.

PubMed: 39328773
DOI: 10.1021/jacsau.4c00404

Experimental method

X-RAY DIFFRACTION (2.35 Å)