Mechanism of ribose 2'-group discrimination by an RNA polymerase

Ying Huang, Fritz Eckstein, Robert Padilla, Rui Sousa

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85 Scopus citations

Abstract

The mechanism by which T7 RNA polymerase (RNAP) discriminates between rNTP and dNTP substrates has been characterized. During transcript elongation T7 RNAP uses rNTPs 70-80-fold more efficiently than dNTPs. Discrimination of the hydrogen-bonding character of the ribose 2'-substituent contributes a largely K(m)-mediated factor of ~20 to this preference for rNTPs. Discrimination of 2'-substituent H-bonding character appears to be made through a hydrogen bond to the hydroxyl group of tyrosine 639. This hydrogen bond makes little net contribution to either rNTP ground or transition state binding energy apparently because it is balanced by the energy of desolvation of the tyrosine hydroxyl. This mechanism may reflect a strategy to facilitate translocation by minimizing contributions from polymerase-NMP moiety interactions to NTP binding energy so as to minimize the affinity of the NTP binding site for the 3'-NMP of the product nucleic acid.

Original languageEnglish (US)
Pages (from-to)8231-8242
Number of pages12
JournalBiochemistry
Volume36
Issue number27
DOIs
StatePublished - Jul 8 1997

ASJC Scopus subject areas

  • Biochemistry

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    Huang, Y., Eckstein, F., Padilla, R., & Sousa, R. (1997). Mechanism of ribose 2'-group discrimination by an RNA polymerase. Biochemistry, 36(27), 8231-8242. https://doi.org/10.1021/bi962674l