MersV1, Main, Exploration, bibRecord, 002B50

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

Identifieur interne : 002B50 ( Main/Exploration ); précédent : 002B49; suivant : 002B51

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

Auteurs : Alexei V. Korennykh [États-Unis] ; Matthew J. Plantinga ; Carl C. Correll ; Joseph A. Piccirilli

Source :

Biochemistry [ 0006-2960 ] ; 2007.

RBID : pubmed:17929942

Descripteurs français

English descriptors

KwdEn :
- Base Sequence, Binding Sites, Catalysis, Endoribonucleases (genetics), Fungal Proteins (chemistry), Fungal Proteins (genetics), Fungal Proteins (metabolism), Models, Biological, Models, Molecular, Models, Theoretical, Molecular Sequence Data, Nucleic Acid Conformation, RNA, Fungal (chemistry), RNA, Fungal (metabolism), Ribonucleases (chemistry), Ribonucleases (metabolism), Structure-Activity Relationship, Substrate Specificity.
MESH :
- chemical , chemistry : Fungal Proteins, RNA, Fungal, Ribonucleases.
- chemical , genetics : Endoribonucleases, Fungal Proteins.
- chemical , metabolism : Fungal Proteins, RNA, Fungal, Ribonucleases.
- Base Sequence, Binding Sites, Catalysis, Models, Biological, Models, Molecular, Models, Theoretical, Molecular Sequence Data, Nucleic Acid Conformation, Structure-Activity Relationship, Substrate Specificity.

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 (k2/K1/2 = 1.1 x 10(9) 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 10(3)-10(6)-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.

DOI: 10.1021/bi700931y
PubMed: 17929942

Affiliations:

Le document en format XML

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<term>Fungal Proteins (genetics)</term>
<term>Fungal Proteins (metabolism)</term>
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<term>Données de séquences moléculaires</term>
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<front><div type="abstract" xml:lang="en">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 (k2/K1/2 = 1.1 x 10(9) 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 10(3)-10(6)-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.</div>
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Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin.

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

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

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Pour générer des pages wiki

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