Literature DB >> 17581653

The role of metal ions in phosphate ester hydrolysis.

Shina C L Kamerlin1, John Wilkie.   

Abstract

Many phosphatases make use of metal ions to aid catalysis of phosphate ester hydrolysis. Here, we investigate the impact of metal ions on the potential energy surface (PES), and hence the preferred reaction mechanism, for a simple model for hydrolysis of phosphate ester monoanions. We show that, while both associative (A(N) + D(N)) and dissociative (D(N) + A(N)) mechanisms are represented on the potential energy surfaces both in the presence and absence of metal ions, the D(N) + A(N) process is favoured when there are no metal ions present and the A(N) + D(N) process is favoured in the presence of two metal ions. A concerted (A(N)D(N)) process is also available in the presence of two metal ions, but proceeds via a high-energy transition state. In the presence of only a single metal ion the A(N)D(N) process is the most favoured, but still proceeds via a high-energy transition state. Thus, we conclude that metallo-enzyme phosphatases are likely to utilise an associative process, while those that function without metal ions may well follow a dissociative process.

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Year:  2007        PMID: 17581653     DOI: 10.1039/b701274h

Source DB:  PubMed          Journal:  Org Biomol Chem        ISSN: 1477-0520            Impact factor:   3.876


  11 in total

1.  The associative nature of adenylyl transfer catalyzed by T4 DNA ligase.

Authors:  Alexey V Cherepanov; Elena V Doroshenko; Jörg Matysik; Simon de Vries; Huub J M de Groot
Journal:  Proc Natl Acad Sci U S A       Date:  2008-06-18       Impact factor: 11.205

2.  A binding free energy decomposition approach for accurate calculations of the fidelity of DNA polymerases.

Authors:  Robert Rucker; Peter Oelschlaeger; Arieh Warshel
Journal:  Proteins       Date:  2010-02-15

3.  Probing mechanism of metal catalyzed hydrolysis of Thymidylyl (3'-O, 5'-S) thymidine phosphodiester derivatives.

Authors:  Mahboobeh Rahimian; Shridhar P Gejji
Journal:  J Mol Model       Date:  2012-11-01       Impact factor: 1.810

4.  Catalytic DNA with phosphatase activity.

Authors:  Jagadeeswaran Chandrasekar; Scott K Silverman
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-18       Impact factor: 11.205

5.  Theoretical investigation of the enzymatic phosphoryl transfer of β-phosphoglucomutase: revisiting both steps of the catalytic cycle.

Authors:  Brigitta Elsässer; Silvia Dohmeier-Fischer; Gregor Fels
Journal:  J Mol Model       Date:  2012-01-12       Impact factor: 1.810

Review 6.  Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  J Phys Chem B       Date:  2009-02-05       Impact factor: 2.991

Review 7.  Why nature really chose phosphate.

Authors:  Shina C L Kamerlin; Pankaz K Sharma; Ram B Prasad; Arieh Warshel
Journal:  Q Rev Biophys       Date:  2013-01-15       Impact factor: 5.318

8.  A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.

Authors:  Shina C L Kamerlin; Charles E McKenna; Myron F Goodman; Myron F Goondman; A Warshel
Journal:  Biochemistry       Date:  2009-06-30       Impact factor: 3.162

9.  Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H.

Authors:  Edina Rosta; H Lee Woodcock; Bernard R Brooks; Gerhard Hummer
Journal:  J Comput Chem       Date:  2009-08       Impact factor: 3.376

10.  Modeling catalytic promiscuity in the alkaline phosphatase superfamily.

Authors:  Fernanda Duarte; Beat Anton Amrein; Shina Caroline Lynn Kamerlin
Journal:  Phys Chem Chem Phys       Date:  2013-06-03       Impact factor: 3.676

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