Stereochemical studies of the .beta.-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys
The DNA strand cleavage reaction catalyzed by endonuclease III from Escherichia coli (endo III) on the 3'-side of aldehyde abasic sites proceeds by a syn beta-elimination involving abstraction of the 2'-pro-S proton and formation of a trans alpha,beta-unsaturated aldose product; we previou...
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| Veröffentlicht in: | Biochemistry (Easton) 1991-01, Vol.30 (4), p.1119-1126 |
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| creator | Mazumder, Abhijit Gerlt, John A Absalon, Michael J Stubbe, JoAnne Cunningham, Richard P Withka, Jane Bolton, Philip H |
| description | The DNA strand cleavage reaction catalyzed by endonuclease III from Escherichia coli (endo III) on the 3'-side of aldehyde abasic sites proceeds by a syn beta-elimination involving abstraction of the 2'-pro-S proton and formation of a trans alpha,beta-unsaturated aldose product; we previously reported the same stereochemical course for the reaction catalyzed by UV endonuclease V from bacteriophage T4 (UV endo V) [Mazumder, A., Gerlt, J. A., Rabow, L., Absalon, M. J., Stubbe, J., & Bolton, P. H. (1989) J. Am. Chem. Soc. 111, 8029-8030]. Since the UV endo V does not contain an 4Fe-4S center, the 4Fe-4S center present in endo III need not be assigned a unique role in the beta-elimination reaction. The beta-elimination reactions that occur under alkaline conditions (0.1 N NaOH) and in the presence of the tripeptide Lys-Trp-Lys proceed by anti beta-elimination mechanisms involving abstraction of the 2'-pro-R proton and formation of a trans alpha,beta-unsaturated aldose product. The different stereochemical outcomes of the enzymatic and nonenzymatic beta-elimination reactions support the hypothesis that the enzyme-catalyzed reactions may involve general-base-catalyzed abstraction of the 2'-pro-S proton by the internucleotidic phosphodiester leaving group. |
| doi_str_mv | 10.1021/bi00218a033 |
| format | Article |
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A., Rabow, L., Absalon, M. J., Stubbe, J., & Bolton, P. H. (1989) J. Am. Chem. Soc. 111, 8029-8030]. Since the UV endo V does not contain an 4Fe-4S center, the 4Fe-4S center present in endo III need not be assigned a unique role in the beta-elimination reaction. The beta-elimination reactions that occur under alkaline conditions (0.1 N NaOH) and in the presence of the tripeptide Lys-Trp-Lys proceed by anti beta-elimination mechanisms involving abstraction of the 2'-pro-R proton and formation of a trans alpha,beta-unsaturated aldose product. The different stereochemical outcomes of the enzymatic and nonenzymatic beta-elimination reactions support the hypothesis that the enzyme-catalyzed reactions may involve general-base-catalyzed abstraction of the 2'-pro-S proton by the internucleotidic phosphodiester leaving group.</description><identifier>ISSN: 0006-2960</identifier><identifier>EISSN: 1520-4995</identifier><identifier>DOI: 10.1021/bi00218a033</identifier><identifier>PMID: 1846560</identifier><language>eng</language><publisher>Washington, DC: American Chemical Society</publisher><subject>Aldehydes - chemistry ; Bacteriology ; Base Sequence ; Biological and medical sciences ; Chromatography, High Pressure Liquid ; Deoxyribonuclease (Pyrimidine Dimer) ; DNA - metabolism ; Endodeoxyribonucleases - metabolism ; Escherichia coli - drug effects ; Escherichia coli - enzymology ; Escherichia coli - genetics ; Escherichia coli Proteins ; Fundamental and applied biological sciences. Psychology ; Hydrogen ; Hydrolysis ; Magnetic Resonance Spectroscopy ; Metabolism. Enzymes ; Microbiology ; Molecular Sequence Data ; Oligopeptides - metabolism ; Phosphoric Diester Hydrolases - chemistry ; Sodium Hydroxide - pharmacology ; Stereoisomerism ; Ultraviolet Rays</subject><ispartof>Biochemistry (Easton), 1991-01, Vol.30 (4), p.1119-1126</ispartof><rights>Copyright © 1991 American Chemical Society</rights><rights>1991 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a481t-43c401997f9233698a42e33ec2e9b7c9349969359222d8bfcdc4b8e30f0e19b53</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/bi00218a033$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/bi00218a033$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>314,776,780,2752,27053,27901,27902,56713,56763</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=19564348$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/1846560$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mazumder, Abhijit</creatorcontrib><creatorcontrib>Gerlt, John A</creatorcontrib><creatorcontrib>Absalon, Michael J</creatorcontrib><creatorcontrib>Stubbe, JoAnne</creatorcontrib><creatorcontrib>Cunningham, Richard P</creatorcontrib><creatorcontrib>Withka, Jane</creatorcontrib><creatorcontrib>Bolton, Philip H</creatorcontrib><title>Stereochemical studies of the .beta.-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys</title><title>Biochemistry (Easton)</title><addtitle>Biochemistry</addtitle><description>The DNA strand cleavage reaction catalyzed by endonuclease III from Escherichia coli (endo III) on the 3'-side of aldehyde abasic sites proceeds by a syn beta-elimination involving abstraction of the 2'-pro-S proton and formation of a trans alpha,beta-unsaturated aldose product; we previously reported the same stereochemical course for the reaction catalyzed by UV endonuclease V from bacteriophage T4 (UV endo V) [Mazumder, A., Gerlt, J. A., Rabow, L., Absalon, M. J., Stubbe, J., & Bolton, P. H. (1989) J. Am. Chem. Soc. 111, 8029-8030]. Since the UV endo V does not contain an 4Fe-4S center, the 4Fe-4S center present in endo III need not be assigned a unique role in the beta-elimination reaction. The beta-elimination reactions that occur under alkaline conditions (0.1 N NaOH) and in the presence of the tripeptide Lys-Trp-Lys proceed by anti beta-elimination mechanisms involving abstraction of the 2'-pro-R proton and formation of a trans alpha,beta-unsaturated aldose product. The different stereochemical outcomes of the enzymatic and nonenzymatic beta-elimination reactions support the hypothesis that the enzyme-catalyzed reactions may involve general-base-catalyzed abstraction of the 2'-pro-S proton by the internucleotidic phosphodiester leaving group.</description><subject>Aldehydes - chemistry</subject><subject>Bacteriology</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Chromatography, High Pressure Liquid</subject><subject>Deoxyribonuclease (Pyrimidine Dimer)</subject><subject>DNA - metabolism</subject><subject>Endodeoxyribonucleases - metabolism</subject><subject>Escherichia coli - drug effects</subject><subject>Escherichia coli - enzymology</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli Proteins</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Hydrogen</subject><subject>Hydrolysis</subject><subject>Magnetic Resonance Spectroscopy</subject><subject>Metabolism. Enzymes</subject><subject>Microbiology</subject><subject>Molecular Sequence Data</subject><subject>Oligopeptides - metabolism</subject><subject>Phosphoric Diester Hydrolases - chemistry</subject><subject>Sodium Hydroxide - pharmacology</subject><subject>Stereoisomerism</subject><subject>Ultraviolet Rays</subject><issn>0006-2960</issn><issn>1520-4995</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>1991</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkUFv1DAQhSMEKkvhxBnJF-BAs9ixncTcylLalVaA1EXiZjnOROuSxFuPI3X_EL8TV1lRDkicnq33-Y01L8teMrpktGDvG0eT1IZy_ihbMFnQXCglH2cLSmmZF6qkT7NniDfpKmglTrITVotSlnSR_bqOEMDbHQzOmp5gnFoHSHxH4g7IsoFoljn0bnCjic6PJICx9wckJhLTt7A7tM4S0xhMgi6m124kn76cfyAwtn6cbA8GgazXa9IFP5ALTOOCsztniPW9OyPoWzcNJCUFf-daOCNmbMnmgPk27POkz7MnnekRXhz1NPv--WK7uso3Xy_Xq_NNbkTNYi64FZQpVXWq4LxUtREFcA62ANVUVvG0l1JxqYqiaOums60VTQ2cdhSYaiQ_zd7MufvgbyfAqAeHFvrejOAn1DUVvJBK_RdkUsm6KmkC382gDR4xQKf3wQ0mHDSj-r4-_Vd9iX51jJ2aAdoHdu4r-a-PvsFUVxfMaB0-YEqWgos6cfnMOYxw98c34acuK15Jvf12rX98XG3kJbvSZeLfzryxqG_8FMa05X_-8Dd8S73x</recordid><startdate>19910101</startdate><enddate>19910101</enddate><creator>Mazumder, Abhijit</creator><creator>Gerlt, John A</creator><creator>Absalon, Michael J</creator><creator>Stubbe, JoAnne</creator><creator>Cunningham, Richard P</creator><creator>Withka, Jane</creator><creator>Bolton, Philip H</creator><general>American Chemical Society</general><scope>BSCLL</scope><scope>IQODW</scope><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>7QL</scope><scope>7TM</scope><scope>C1K</scope><scope>7X8</scope></search><sort><creationdate>19910101</creationdate><title>Stereochemical studies of the .beta.-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys</title><author>Mazumder, Abhijit ; Gerlt, John A ; Absalon, Michael J ; Stubbe, JoAnne ; Cunningham, Richard P ; Withka, Jane ; Bolton, Philip H</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a481t-43c401997f9233698a42e33ec2e9b7c9349969359222d8bfcdc4b8e30f0e19b53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>1991</creationdate><topic>Aldehydes - chemistry</topic><topic>Bacteriology</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Chromatography, High Pressure Liquid</topic><topic>Deoxyribonuclease (Pyrimidine Dimer)</topic><topic>DNA - metabolism</topic><topic>Endodeoxyribonucleases - metabolism</topic><topic>Escherichia coli - drug effects</topic><topic>Escherichia coli - enzymology</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli Proteins</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Hydrogen</topic><topic>Hydrolysis</topic><topic>Magnetic Resonance Spectroscopy</topic><topic>Metabolism. Enzymes</topic><topic>Microbiology</topic><topic>Molecular Sequence Data</topic><topic>Oligopeptides - metabolism</topic><topic>Phosphoric Diester Hydrolases - chemistry</topic><topic>Sodium Hydroxide - pharmacology</topic><topic>Stereoisomerism</topic><topic>Ultraviolet Rays</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mazumder, Abhijit</creatorcontrib><creatorcontrib>Gerlt, John A</creatorcontrib><creatorcontrib>Absalon, Michael J</creatorcontrib><creatorcontrib>Stubbe, JoAnne</creatorcontrib><creatorcontrib>Cunningham, Richard P</creatorcontrib><creatorcontrib>Withka, Jane</creatorcontrib><creatorcontrib>Bolton, Philip H</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Nucleic Acids Abstracts</collection><collection>Environmental Sciences and Pollution Management</collection><collection>MEDLINE - Academic</collection><jtitle>Biochemistry (Easton)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mazumder, Abhijit</au><au>Gerlt, John A</au><au>Absalon, Michael J</au><au>Stubbe, JoAnne</au><au>Cunningham, Richard P</au><au>Withka, Jane</au><au>Bolton, Philip H</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Stereochemical studies of the .beta.-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys</atitle><jtitle>Biochemistry (Easton)</jtitle><addtitle>Biochemistry</addtitle><date>1991-01-01</date><risdate>1991</risdate><volume>30</volume><issue>4</issue><spage>1119</spage><epage>1126</epage><pages>1119-1126</pages><issn>0006-2960</issn><eissn>1520-4995</eissn><abstract>The DNA strand cleavage reaction catalyzed by endonuclease III from Escherichia coli (endo III) on the 3'-side of aldehyde abasic sites proceeds by a syn beta-elimination involving abstraction of the 2'-pro-S proton and formation of a trans alpha,beta-unsaturated aldose product; we previously reported the same stereochemical course for the reaction catalyzed by UV endonuclease V from bacteriophage T4 (UV endo V) [Mazumder, A., Gerlt, J. A., Rabow, L., Absalon, M. J., Stubbe, J., & Bolton, P. H. (1989) J. Am. Chem. Soc. 111, 8029-8030]. Since the UV endo V does not contain an 4Fe-4S center, the 4Fe-4S center present in endo III need not be assigned a unique role in the beta-elimination reaction. The beta-elimination reactions that occur under alkaline conditions (0.1 N NaOH) and in the presence of the tripeptide Lys-Trp-Lys proceed by anti beta-elimination mechanisms involving abstraction of the 2'-pro-R proton and formation of a trans alpha,beta-unsaturated aldose product. The different stereochemical outcomes of the enzymatic and nonenzymatic beta-elimination reactions support the hypothesis that the enzyme-catalyzed reactions may involve general-base-catalyzed abstraction of the 2'-pro-S proton by the internucleotidic phosphodiester leaving group.</abstract><cop>Washington, DC</cop><pub>American Chemical Society</pub><pmid>1846560</pmid><doi>10.1021/bi00218a033</doi><tpages>8</tpages></addata></record> |
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| subjects | Aldehydes - chemistry Bacteriology Base Sequence Biological and medical sciences Chromatography, High Pressure Liquid Deoxyribonuclease (Pyrimidine Dimer) DNA - metabolism Endodeoxyribonucleases - metabolism Escherichia coli - drug effects Escherichia coli - enzymology Escherichia coli - genetics Escherichia coli Proteins Fundamental and applied biological sciences. Psychology Hydrogen Hydrolysis Magnetic Resonance Spectroscopy Metabolism. Enzymes Microbiology Molecular Sequence Data Oligopeptides - metabolism Phosphoric Diester Hydrolases - chemistry Sodium Hydroxide - pharmacology Stereoisomerism Ultraviolet Rays |
| title | Stereochemical studies of the .beta.-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys |
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