Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin.
Identifieur interne : 002155 ( PubMed/Corpus ); précédent : 002154; suivant : 002156Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin.
Auteurs : Alexei V. Korennykh ; Matthew J. Plantinga ; Carl C. Correll ; Joseph A. PiccirilliSource :
- Biochemistry [ 0006-2960 ] ; 2007.
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
Links to Exploration step
pubmed:17929942Le document en format XML
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Piccirilli</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2007">2007</date><idno type="RBID">pubmed:17929942</idno><idno type="pmid">17929942</idno><idno type="doi">10.1021/bi700931y</idno><idno type="wicri:Area/PubMed/Corpus">002155</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002155</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin.</title><author><name sortKey="Korennykh, Alexei V" sort="Korennykh, Alexei V" uniqKey="Korennykh A" first="Alexei V" last="Korennykh">Alexei V. Korennykh</name><affiliation><nlm:affiliation>Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Plantinga, Matthew J" sort="Plantinga, Matthew J" uniqKey="Plantinga M" first="Matthew J" last="Plantinga">Matthew J. Plantinga</name></author><author><name sortKey="Correll, Carl C" sort="Correll, Carl C" uniqKey="Correll C" first="Carl C" last="Correll">Carl C. Correll</name></author><author><name sortKey="Piccirilli, Joseph A" sort="Piccirilli, Joseph A" uniqKey="Piccirilli J" first="Joseph A" last="Piccirilli">Joseph A. Piccirilli</name></author></analytic><series><title level="j">Biochemistry</title><idno type="ISSN">0006-2960</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Binding Sites</term><term>Catalysis</term><term>Endoribonucleases (genetics)</term><term>Fungal Proteins (chemistry)</term><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Models, Biological</term><term>Models, Molecular</term><term>Models, Theoretical</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>RNA, Fungal (chemistry)</term><term>RNA, Fungal (metabolism)</term><term>Ribonucleases (chemistry)</term><term>Ribonucleases (metabolism)</term><term>Structure-Activity Relationship</term><term>Substrate Specificity</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Fungal Proteins</term><term>RNA, Fungal</term><term>Ribonucleases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Endoribonucleases</term><term>Fungal Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fungal Proteins</term><term>RNA, Fungal</term><term>Ribonucleases</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Binding Sites</term><term>Catalysis</term><term>Models, Biological</term><term>Models, Molecular</term><term>Models, Theoretical</term><term>Molecular Sequence Data</term><term>Nucleic Acid Conformation</term><term>Structure-Activity Relationship</term><term>Substrate Specificity</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17929942</PMID><DateCompleted><Year>2008</Year><Month>01</Month><Day>11</Day></DateCompleted><DateRevised><Year>2016</Year><Month>11</Month><Day>24</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0006-2960</ISSN><JournalIssue CitedMedium="Print"><Volume>46</Volume><Issue>44</Issue><PubDate><Year>2007</Year><Month>Nov</Month><Day>06</Day></PubDate></JournalIssue><Title>Biochemistry</Title><ISOAbbreviation>Biochemistry</ISOAbbreviation></Journal><ArticleTitle>Linkage between substrate recognition and catalysis during cleavage of sarcin/ricin loop RNA by restrictocin.</ArticleTitle><Pagination><MedlinePgn>12744-56</MedlinePgn></Pagination><Abstract><AbstractText>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.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Korennykh</LastName><ForeName>Alexei V</ForeName><Initials>AV</Initials><AffiliationInfo><Affiliation>Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Plantinga</LastName><ForeName>Matthew J</ForeName><Initials>MJ</Initials></Author><Author ValidYN="Y"><LastName>Correll</LastName><ForeName>Carl C</ForeName><Initials>CC</Initials></Author><Author ValidYN="Y"><LastName>Piccirilli</LastName><ForeName>Joseph A</ForeName><Initials>JA</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>GM59782</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2007</Year><Month>10</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biochemistry</MedlineTA><NlmUniqueID>0370623</NlmUniqueID><ISSNLinking>0006-2960</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012331">RNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>1407-48-3</RegistryNumber><NameOfSubstance UI="C014801">alpha-sarcin</NameOfSubstance></Chemical><Chemical><RegistryNumber>1F8KS5O261</RegistryNumber><NameOfSubstance UI="C036196">MITF protein, Aspergillus restrictus</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.-</RegistryNumber><NameOfSubstance UI="D004722">Endoribonucleases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.-</RegistryNumber><NameOfSubstance UI="D012260">Ribonucleases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002384" MajorTopicYN="N">Catalysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004722" MajorTopicYN="N">Endoribonucleases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008954" MajorTopicYN="N">Models, Biological</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008962" MajorTopicYN="N">Models, Theoretical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="Y">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012331" MajorTopicYN="N">RNA, 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