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Mechanism of Mg 2+ -accompanied product release in sugar nucleotidyltransferases
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Vithani, Neha, Jagtap, Pravin Kumar Ankush, Verma, Sunil Kumar, Tripathi, Ravi, Awasthi, Shalini, Nair, Nisanth N. and Prakash, Balaji (2018) Mechanism of Mg 2+ -accompanied product release in sugar nucleotidyltransferases. Structure, 26 (3). pp. 459-466. doi:10.1016/j.str.2018.02.002 ISSN 0969-2126.
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Official URL: http://dx.doi.org/10.1016/j.str.2018.02.002
Abstract
The nucleotidyl transfer reaction, catalyzed by sugar nucleotidyltransferases (SNTs), is assisted by two active site Mg 2+ ions. While studying this reaction using X-ray crystallography, we captured snapshots of the pyrophosphate (product) as it exits along a pocket. Surprisingly, one of the active site Mg 2+ ions remains coordinated to the exiting pyrophosphate. This hints at the participation of Mg 2+ in the process of product release, besides its role in catalyzing nucleotidyl transfer. These observations are further supported by enhanced sampling molecular dynamics simulations. Free energy computations suggest that the product release is likely to be rate limiting in SNTs, and the origin of the high free energy barrier for product release could be traced back to the “slow” conformational change of an Arg residue at the exit end of the pocket. These results establish a dual role for Mg 2+, and propose a general mechanism of product release during the nucleotidyl transfer by SNTs.
Item Type: | Journal Article | ||||||
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Alternative Title: | Mechanism of Mg2+-Accompanied Product Release in Sugar Nucleotidyltransferases | ||||||
Subjects: | Q Science > QP Physiology | ||||||
Divisions: | Faculty of Science, Engineering and Medicine > Engineering > WMG (Formerly the Warwick Manufacturing Group) | ||||||
Library of Congress Subject Headings (LCSH): | Molecular dynamics, Nucleotides, Pyrophosphates | ||||||
Journal or Publication Title: | Structure | ||||||
Publisher: | Cell Press | ||||||
ISSN: | 0969-2126 | ||||||
Official Date: | 6 March 2018 | ||||||
Dates: |
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Volume: | 26 | ||||||
Number: | 3 | ||||||
Page Range: | pp. 459-466 | ||||||
DOI: | 10.1016/j.str.2018.02.002 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||
Date of first compliant deposit: | 3 September 2018 | ||||||
Date of first compliant Open Access: | 6 March 2019 | ||||||
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