Effect of Chemically Distinct Substrates on the Mechanism and Reactivity of a Highly Promiscuous Metallohydrolase

Gaurav Sharma, Vindi M. Jayasinghe-Arachchige, Qiaoyu Hu, Gerhard Schenk, Rajeev Prabhakar

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


In this DFT study, the substrate promiscuity of the binuclear [Fe(II)-Zn(II)] core containing glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes has been investigated through the hydrolysis of three chemically diverse groups of substrates: i.e., phosphomono-, phosphodi-, and phosphotriesters. The hydrolysis of these substrates is studied by comparing stepwise, concerted, and substrate-assisted mechanisms. Both the stepwise and concerted mechanisms occur with similar barriers, while the energetics for the substrate-assisted mechanism are significantly less favorable. Irrespective of the mechanism, active site residue His217 plays a critical role, in agreement with structural, kinetics, and spectroscopic data, but the transition state of the reaction depends on the identity of the substrate (dissociative for the triester paraoxon, associative for the monoester 4-nitrophenyl phosphate (NPP), and in-between for the diesters glycerol-3-phosphoethanolamine (GPE) and bis(4-nitrophenyl)phosphate (BNPP)). In good agreement with available kinetic and spectrophotometric data, the calculations highlight the preference of GpdQ for diester substrates, followed by tri- and monoesters. For substrates with two different types of scissile bonds (paraoxon and GPE) a clear preference for the bond with the stronger electron withdrawing leaving group was observed. The extensive agreement between experimental data and DFT calculations enhances the understanding of the mechanism of GpdQ-catalyzed hydrolysis and paves the way for the rational design of optimized catalysts for the hydrolysis of different types of phosphoesters.

Original languageEnglish (US)
Pages (from-to)3684-3696
Number of pages13
JournalACS Catalysis
Issue number6
StatePublished - Mar 20 2020


  • glycerophosphodiesterase (GpdQ)
  • metallohydrolase
  • phosphoester hydrolysis
  • reaction mechanisms and density functional theory (DFT)
  • substrate promiscuity

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)


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