4M1J

Crystal structure of Pseudomonas aeruginosa PvdQ in complex with a transition state analogue

Summary for 4M1J

• Entry DOI: 10.2210/pdb4m1j/pdb
• Descriptor: Acyl-homoserine lactone acylase PvdQ subunit beta, Acyl-homoserine lactone acylase PvdQ subunit alpha, tridecylboronic acid, ... (5 entities in total)
• Functional Keywords: transition state analogue, heterodimer, acylase, boronic acid, secreted, hydrolase
• Biological source: Pseudomonas aeruginosa; More
• Cellular location: Periplasm : Q9I194 Q9I194
• Total number of polymer chains: 2
• Total formula weight: 80695.33

Authors

Wu, R.,Clevenger, K.,Er, J.,Fast, W.L.,Liu, D. (deposition date: 2013-08-02, release date: 2013-08-28, Last modification date: 2024-11-06)

Primary citation

Clevenger, K.D.,Wu, R.,Er, J.A.,Liu, D.,Fast, W.
Rational Design of a Transition State Analogue with Picomolar Affinity for Pseudomonas aeruginosa PvdQ, a Siderophore Biosynthetic Enzyme.
Acs Chem.Biol., 8:2192-2200, 2013

PubMed Abstract: The Pseudomonas aeruginosa enzyme PvdQ can process different substrates involved in quorum-sensing or in siderophore biosynthesis. Substrate selectivity was evaluated using steady-state kinetic constants for hydrolysis of N-acyl-homoserine lactones (HSLs) and p-nitrophenyl fatty acid esters. PvdQ prefers substrates with alkyl chains between 12 and 14 carbons long that do not bear a 3-oxo substitution and is revealed here to have a relatively high specificity constant for selected N-acyl-HSLs (kcat/KM = 10(5) to 10(6) M(-1) s(-1)). However, endogenous P. aeruginosa N-acyl-HSLs are ≥100-fold disfavored, supporting the conclusion that PvdQ was not primarily evolved to regulate endogenous quorum-sensing. PvdQ plays an essential biosynthetic role for the siderophore pyoverdine, on which P. aeruginosa depends for growth in iron-limited environments. A series of alkylboronate inhibitors was found to be reversible, competitive, and extremely potent (Ki ≥ 190 pM). A 1.8 Å X-ray structure shows that 1-tridecylboronic acid forms a monocovalent bond with the N-terminal β-chain Ser residue in the PvdQ heterodimer, mimicking a reaction transition state. This boronic acid inhibits growth of P. aeruginosa in iron-limited media, reproducing the phenotype of a genetic pvdQ disruption, although co-administration of an efflux pump inhibitor is required to maintain growth inhibition. These findings support the strategy of designing boron-based inhibitors of siderophore biosynthetic enzymes to control P. aeruginosa infections.

PubMed: 23883096
DOI: 10.1021/cb400345h

Experimental method

X-RAY DIFFRACTION (1.8 Å)