Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch
The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-Å X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA–ligand recognition. To...
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| Veröffentlicht in: | Journal of molecular biology 2010-02, Vol.396 (3), p.761-772 |
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| creator | Montange, Rebecca K. Mondragón, Estefanía van Tyne, Daria Garst, Andrew D. Ceres, Pablo Batey, Robert T. |
| description | The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-Å X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA–ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-Å improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH. |
| doi_str_mv | 10.1016/j.jmb.2009.12.007 |
| format | Article |
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We previously determined the 2.9-Å X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA–ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-Å improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.</description><identifier>ISSN: 0022-2836</identifier><identifier>EISSN: 1089-8638</identifier><identifier>DOI: 10.1016/j.jmb.2009.12.007</identifier><identifier>PMID: 20006621</identifier><language>eng</language><publisher>England: Elsevier Ltd</publisher><subject>Adenosine - analogs & derivatives ; Adenosine - metabolism ; AFFINITY ; Base Pairing ; BASIC BIOLOGICAL SCIENCES ; CALORIMETRY ; Conserved Sequence ; CRYSTAL STRUCTURE ; CRYSTALLOGRAPHY ; Crystallography, X-Ray ; ELECTROSTATICS ; GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE ; GENETIC CONTROL ; isothermal titration calorimetry ; Kinetics ; METABOLITES ; Models, Molecular ; MUTANTS ; Mutation ; national synchrotron light source ; non-protein-coding RNA ; Nucleic Acid Conformation ; RESOLUTION ; riboregulation ; RNA ; RNA, Bacterial - chemistry ; RNA, Bacterial - genetics ; RNA, Bacterial - metabolism ; RNA, Messenger - chemistry ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; S-Adenosylhomocysteine - metabolism ; S-adenosylmethionine ; S-Adenosylmethionine - metabolism ; SPECIFICITY ; TITRATION ; X-ray crystallography</subject><ispartof>Journal of molecular biology, 2010-02, Vol.396 (3), p.761-772</ispartof><rights>2009 Elsevier Ltd</rights><rights>Copyright (c) 2009. Elsevier Ltd. All rights reserved.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c477t-92d696567fdefd1f643463a89230de2e7ca219f4be9feaef4601843cacc584d43</citedby><cites>FETCH-LOGICAL-c477t-92d696567fdefd1f643463a89230de2e7ca219f4be9feaef4601843cacc584d43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0022283609014776$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>230,314,776,780,881,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20006621$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/biblio/1019815$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Montange, Rebecca K.</creatorcontrib><creatorcontrib>Mondragón, Estefanía</creatorcontrib><creatorcontrib>van Tyne, Daria</creatorcontrib><creatorcontrib>Garst, Andrew D.</creatorcontrib><creatorcontrib>Ceres, Pablo</creatorcontrib><creatorcontrib>Batey, Robert T.</creatorcontrib><creatorcontrib>Brookhaven National Laboratory (BNL) National Synchrotron Light Source</creatorcontrib><title>Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch</title><title>Journal of molecular biology</title><addtitle>J Mol Biol</addtitle><description>The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-Å X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA–ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-Å improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.</description><subject>Adenosine - analogs & derivatives</subject><subject>Adenosine - metabolism</subject><subject>AFFINITY</subject><subject>Base Pairing</subject><subject>BASIC BIOLOGICAL SCIENCES</subject><subject>CALORIMETRY</subject><subject>Conserved Sequence</subject><subject>CRYSTAL STRUCTURE</subject><subject>CRYSTALLOGRAPHY</subject><subject>Crystallography, X-Ray</subject><subject>ELECTROSTATICS</subject><subject>GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE</subject><subject>GENETIC CONTROL</subject><subject>isothermal titration calorimetry</subject><subject>Kinetics</subject><subject>METABOLITES</subject><subject>Models, Molecular</subject><subject>MUTANTS</subject><subject>Mutation</subject><subject>national synchrotron light source</subject><subject>non-protein-coding RNA</subject><subject>Nucleic Acid Conformation</subject><subject>RESOLUTION</subject><subject>riboregulation</subject><subject>RNA</subject><subject>RNA, Bacterial - chemistry</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Bacterial - metabolism</subject><subject>RNA, Messenger - chemistry</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>S-Adenosylhomocysteine - metabolism</subject><subject>S-adenosylmethionine</subject><subject>S-Adenosylmethionine - metabolism</subject><subject>SPECIFICITY</subject><subject>TITRATION</subject><subject>X-ray crystallography</subject><issn>0022-2836</issn><issn>1089-8638</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9UctqGzEUFaWhcZN-QDdFdJPVTPWyRkOhENxXICGQtGuhke7UMrKUjuQE_301OA3tJist7jlH54HQW0paSqj8sGk326FlhPQtZS0h3Qu0oET1jZJcvUQLQhhrmOLyGL3OeUMIWXKhXqHjSiFSMrpAt599tpPf-miKTxEPUB4AIl6FlCHs8Q0EU8DhFYSwC2bCV1DMkIIvkPGwx2UN-Pb8qrnAN35I-cEXuz5FR6MJGd48vifo59cvP1bfm8vrbxer88vGiq4rTc-c7OVSdqOD0dFRCi4kN6pnnDhg0FnDaD-KAfoRDIxCEqoEt8bapRJO8BP06aB7txu24CzEMpmg72ocM-11Ml7_f4l-rX-le80UYx2dBd4fBFIuXmdbQ9m1TTGCLbo23Cu6rKCzx1-m9HsHuehtrazWYSKkXdYd510dg8iKpAeknVLOE4xPViiZ5aTe6DqYngfTlOk6WOW8-zfDE-PvQhXw8QCA2uS9h2n2CdGC89Ns0yX_jPwf77CnIA</recordid><startdate>20100226</startdate><enddate>20100226</enddate><creator>Montange, Rebecca K.</creator><creator>Mondragón, Estefanía</creator><creator>van Tyne, Daria</creator><creator>Garst, Andrew D.</creator><creator>Ceres, Pablo</creator><creator>Batey, Robert T.</creator><general>Elsevier Ltd</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>OTOTI</scope><scope>5PM</scope></search><sort><creationdate>20100226</creationdate><title>Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch</title><author>Montange, Rebecca K. ; Mondragón, Estefanía ; van Tyne, Daria ; Garst, Andrew D. ; Ceres, Pablo ; Batey, Robert T.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c477t-92d696567fdefd1f643463a89230de2e7ca219f4be9feaef4601843cacc584d43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Adenosine - analogs & derivatives</topic><topic>Adenosine - metabolism</topic><topic>AFFINITY</topic><topic>Base Pairing</topic><topic>BASIC BIOLOGICAL SCIENCES</topic><topic>CALORIMETRY</topic><topic>Conserved Sequence</topic><topic>CRYSTAL STRUCTURE</topic><topic>CRYSTALLOGRAPHY</topic><topic>Crystallography, X-Ray</topic><topic>ELECTROSTATICS</topic><topic>GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE</topic><topic>GENETIC CONTROL</topic><topic>isothermal titration calorimetry</topic><topic>Kinetics</topic><topic>METABOLITES</topic><topic>Models, Molecular</topic><topic>MUTANTS</topic><topic>Mutation</topic><topic>national synchrotron light source</topic><topic>non-protein-coding RNA</topic><topic>Nucleic Acid Conformation</topic><topic>RESOLUTION</topic><topic>riboregulation</topic><topic>RNA</topic><topic>RNA, Bacterial - chemistry</topic><topic>RNA, Bacterial - genetics</topic><topic>RNA, Bacterial - metabolism</topic><topic>RNA, Messenger - chemistry</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>S-Adenosylhomocysteine - metabolism</topic><topic>S-adenosylmethionine</topic><topic>S-Adenosylmethionine - metabolism</topic><topic>SPECIFICITY</topic><topic>TITRATION</topic><topic>X-ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Montange, Rebecca K.</creatorcontrib><creatorcontrib>Mondragón, Estefanía</creatorcontrib><creatorcontrib>van Tyne, Daria</creatorcontrib><creatorcontrib>Garst, Andrew D.</creatorcontrib><creatorcontrib>Ceres, Pablo</creatorcontrib><creatorcontrib>Batey, Robert T.</creatorcontrib><creatorcontrib>Brookhaven National Laboratory (BNL) National Synchrotron Light Source</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>OSTI.GOV</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of molecular biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Montange, Rebecca K.</au><au>Mondragón, Estefanía</au><au>van Tyne, Daria</au><au>Garst, Andrew D.</au><au>Ceres, Pablo</au><au>Batey, Robert T.</au><aucorp>Brookhaven National Laboratory (BNL) National Synchrotron Light Source</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch</atitle><jtitle>Journal of molecular biology</jtitle><addtitle>J Mol Biol</addtitle><date>2010-02-26</date><risdate>2010</risdate><volume>396</volume><issue>3</issue><spage>761</spage><epage>772</epage><pages>761-772</pages><issn>0022-2836</issn><eissn>1089-8638</eissn><abstract>The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-Å X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA–ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-Å improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. 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| ispartof | Journal of molecular biology, 2010-02, Vol.396 (3), p.761-772 |
| issn | 0022-2836 1089-8638 |
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| subjects | Adenosine - analogs & derivatives Adenosine - metabolism AFFINITY Base Pairing BASIC BIOLOGICAL SCIENCES CALORIMETRY Conserved Sequence CRYSTAL STRUCTURE CRYSTALLOGRAPHY Crystallography, X-Ray ELECTROSTATICS GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE GENETIC CONTROL isothermal titration calorimetry Kinetics METABOLITES Models, Molecular MUTANTS Mutation national synchrotron light source non-protein-coding RNA Nucleic Acid Conformation RESOLUTION riboregulation RNA RNA, Bacterial - chemistry RNA, Bacterial - genetics RNA, Bacterial - metabolism RNA, Messenger - chemistry RNA, Messenger - genetics RNA, Messenger - metabolism S-Adenosylhomocysteine - metabolism S-adenosylmethionine S-Adenosylmethionine - metabolism SPECIFICITY TITRATION X-ray crystallography |
| title | Discrimination between Closely Related Cellular Metabolites by the SAM-I Riboswitch |
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