Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme

Moshe Ben-David, Grzegorz Wieczorek, Mikael Elias, Israel Silman, Joel L. Sussman, Dan S. Tawfik

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51 Scopus citations


Although largely deemed as structurally conserved, catalytic metal ion sites can rearrange, thereby contributing to enzyme evolvability. Here, we show that in paraoxonase-1, a lipo-lactonase, catalytic promiscuity and divergence into an organophosphate hydrolase are correlated with an alternative mode of the catalytic Ca2 +. We describe the crystal structures of active-site mutants bearing mutations at position 115. The histidine at this position acts as a base to activate the lactone-hydrolyzing water molecule. Mutations to Trp or Gln indeed diminish paraoxonase-1's lactonase activity; however, the promiscuous organophosphate hydrolase activity is enhanced. The structures reveal a 1.8-Å upward displacement towards the enzyme's surface of the catalytic Ca2 + in the His115 mutants and configurational changes in the ligating side chains and water molecules, relative to the wild-type enzyme. Biochemical analysis and molecular dynamics simulations suggest that this alternative, upward metal mode mediates the promiscuous hydrolysis of organophosphates. The upward Ca2 + mode observed in the His115 mutants also appears to mediate the wild type's paraoxonase activity. However, whereas the upward mode dominates in the Trp115 mutant, it is scarcely populated in wild type. Thus, the plasticity of active-site metal ions may permit alternative, latent, promiscuous activities and also provide the basis for the divergence of new enzymatic functions.

Original languageEnglish (US)
Pages (from-to)1028-1038
Number of pages11
JournalJournal of Molecular Biology
Issue number6
StatePublished - 2013

Bibliographical note

Funding Information:
We are grateful to the Israel Structural Proteomics Centre for access to its protein purification and crystallization facilities. We thank Tom Magliery and Chris Hadad (Ohio State University) for sharing their preliminary results and for fruitful discussions. Financial support by the National Institutes of Health ( 2-U54-NS058183 ), the Defense Threat Reduction Agency ( HDTRA1-11-C-0026 ), and the Benoziyo Center for Neuroscience are gratefully acknowledged. D.S.T. is the Nella and Leon Benoziyo Professor of Biochemistry. J.L.S. is the Pickman Professor of Structural Biology.


  • catalytic calcium
  • catalytic promiscuity
  • conformational diversity
  • enzyme catalysis
  • metal catalysis


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