Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin

Alexei V. Korennykh, Matthew J. Plantinga, Carl C. Correll, Joseph A. Piccirilli

Research output: Contribution to journalArticle

16 Scopus citations

Abstract

Restrictocin is a site-specific endoribonuclease that inactivates ribosomes by cleaving the sarcin/ricin loop (SRL) of 23S-28S rRNA. Here we present a kinetic and thermodynamic analysis of the SRL cleavage reaction based on monitoring the cleavage of RNA oligonucleotides (2-27-mers). Restrictocin binds to a 27-mer SRL model substrate (designated wild-type SRL) via electrostatic interactions to form a nonspecific ground state complex E:S. At pH 6.7, physical steps govern the reaction rate: the wild-type substrate reacts at a partially diffusion-limited rate, and a faster-reacting SRL, containing a 3′-sulfur atom at the scissile phosphate, reacts at a fully diffusion-limited rate (k 2/K1/2 = 1.1 × 109 M-1 s -1)• At pH 7.4, the chemical step apparently limits the SRL cleavage rate. After the nonspecific binding step, restrictocin recognizes the SRL structure, which imparts 4.3 kcal/mol transition state stabilization relative to a single-stranded RNA. The two conserved SRL modules, bulged-G motif and GAGA tetraloop, contribute at least 2.4 and 1.9 kcal/mol, respectively, to the recognition. These findings suggest a model of SRL recognition in which restrictocin contacts the GAGA tetraloop and the bulged guanosine of the bulged-G motif to progress from the nonspecific ground state complex (E:S) to the higher-energy-specific complex (E·S) en route to the chemical transition state. Comparison of restrictocin with other ribonucleases revealed that restrictocin exhibits a 103-106-fold smaller ribonuclease activity against single-stranded RNA than do the restrictocin homologues, non-structure-specific ribonucleases T1 and U2. Together, these findings show how structural features of the SRL substrate facilitate catalysis and provide a mechanism for distinguishing between cognate and noncognate RNA.

Original languageEnglish (US)
Pages (from-to)12744-12756
Number of pages13
JournalBiochemistry
Volume46
Issue number44
DOIs
StatePublished - Nov 6 2007
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Biochemistry

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    Korennykh, A. V., Plantinga, M. J., Correll, C. C., & Piccirilli, J. A. (2007). Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin. Biochemistry, 46(44), 12744-12756. https://doi.org/10.1021/bi700931y