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Central role of the RNA polymerase trigger loop in intrinsic RNA hydrolysis

Lookup NU author(s): Dr Yulia Yuzenkova, Professor Nikolay ZenkinORCiD


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The active center of RNA polymerase can hydrolyze phosphodiester bonds in nascent RNA, a reaction thought to be important for proofreading of transcription. The reaction proceeds via a general two Mg2+ mechanism and is assisted by the 3' end nucleotide of the transcript. Here, by using Thermus aquaticus RNA polymerase, we show that the reaction also requires the flexible domain of the active center, the trigger loop (TL). We show that the invariant histidine (beta' His1242) of the TL is essential for hydrolysis/proof-reading and participates in the reaction in two distinct ways: by positioning the 3' end nucleotide of the transcript that assists catalysis and/or by directly participating in the reaction as a general base. We also show that participation of the beta' His1242 of the TL in phosphodiester bond hydrolysis does not depend on the extent of elongation complex backtracking. We obtained similar results with Escherichia coli RNA polymerase, indicating that the function of the TL in phosphodiester bond hydrolysis is conserved among bacteria.

Publication metadata

Author(s): Yuzenkova Y, Zenkin N

Publication type: Article

Publication status: Published

Journal: Proceedings of the National Academy of Sciences

Year: 2010

Volume: 107

Issue: 24

Pages: 10878-10883

Print publication date: 01/06/2010

ISSN (print): 0027-8424

ISSN (electronic): 1091-6490

Publisher: National Academy of Sciences


DOI: 10.1073/pnas.0914424107


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Funder referenceFunder name
Royal Society
United Kingdom Biotechnology and Biological Sciences Research Council
ERC-2007-StG202994-MTPEuropean Research Council