4WKU: N-alkylboronic Acid Inhibitors Reveal Determinants Of Ligand Specificity In The Quorum-quenching And Siderophore Biosynthetic Enzyme Pvdq

The enzyme PvdQ (E.C. from Pseudomonas aeruginosa is an N-terminal nucleophile hydrolase that catalyzes the removal of an N-myristyl substituent from a biosynthetic precursor of the iron-chelating siderophore pyoverdine. Inhibitors of pyoverdine biosynthesis are potential antibiotics since iron is essential for growth and scarce in most infections. PvdQ also catalyzes hydrolytic amide bond cleavage of selected N-acyl-l-homoserine lactone quorum-sensing signals used by some Gram-negative pathogens to coordinate the transcription of virulence factors. The resulting quorum-quenching activity of PvdQ has potential applications in antivirulence therapies. To inform both inhibitor design and enzyme engineering efforts, a series of n-alkylboronic acid inhibitors of PvdQ was characterized to reveal determinants of ligand selectivity. A simple homologation series results in compounds with Ki values that span from 4.7 mM to 190 pM, with a dependence of DeltaGbind values on chain length of -1.0 kcal/mol/CH2. X-ray crystal structures are determined for the PvdQ complexes with 1-ethyl-, 1-butyl-, 1-hexyl-, and 1-octylboronic acids at 1.6, 1.8, 2.0, and 2.1 A resolution, respectively. The 1-hexyl- and 1-octylboronic acids form tetrahedral adducts with the active-site N-terminal Ser217 in the beta-subunit of PvdQ, and the n-alkyl substituents are bound in the acyl-group binding site. The 1-ethyl- and 1-butylboronic acids also form adducts with Ser217 but instead form trigonal planar adducts and extend their n-alkyl substituents into an alternative binding site. These results are interpreted to propose a ligand discrimination model for PvdQ that informs the development of PvdQ-related tools and therapeutics.
PDB ID: 4WKUDownload
MMDB ID: 124757
PDB Deposition Date: 2014/10/3
Updated in MMDB: 2014/11
Experimental Method:
x-ray diffraction
Resolution: 2  Å
Source Organism:
Similar Structures:
Biological Unit for 4WKU: dimeric; determined by author and by software (PISA)
Molecular Components in 4WKU
Label Count Molecule
Proteins (2 molecules)
Acyl-homoserine Lactone Acylase Pvdq(Gene symbol: pvdQ)
Molecule annotation
Acyl-homoserine Lactone Acylase Pvdq(Gene symbol: pvdQ)
Molecule annotation
Chemicals (17 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB