Characterization of Runella slithyformis HD-Pnk, a Bifunctional DNA/RNA End-Healing Enzyme Composed of an N-Terminal 2',3'-Phosphoesterase HD Domain and a C-Terminal 5'-OH Polynucleotide Kinase Domain.
Identifieur interne : 000E76 ( PubMed/Curation ); précédent : 000E75; suivant : 000E77Characterization of Runella slithyformis HD-Pnk, a Bifunctional DNA/RNA End-Healing Enzyme Composed of an N-Terminal 2',3'-Phosphoesterase HD Domain and a C-Terminal 5'-OH Polynucleotide Kinase Domain.
Auteurs : Annum Munir [États-Unis] ; Stewart Shuman [Kiribati]Source :
- Journal of bacteriology [ 1098-5530 ] ; 2017.
Abstract
5'- and 3'-end-healing reactions are key steps in nucleic acid break repair in which 5'-OH ends are phosphorylated by a polynucleotide kinase (Pnk) and 3'-PO4 or 2',3'-cyclic-PO4 ends are hydrolyzed by a phosphoesterase to generate the 5'-PO4 and 3'-OH termini required for sealing by classic polynucleotide ligases. End-healing and sealing enzymes are present in diverse bacterial taxa, often organized as modular units within a single multifunctional polypeptide or as subunits of a repair complex. Here we identify and characterize Runella slithyformis HD-Pnk as a novel bifunctional end-healing enzyme composed of an N-terminal 2',3'-phosphoesterase HD domain and a C-terminal 5'-OH polynucleotide kinase P-loop domain. HD-Pnk phosphorylates 5'-OH polynucleotides (9-mers or longer) in the presence of magnesium and any nucleoside triphosphate donor. HD-Pnk dephosphorylates RNA 2',3'-cyclic phosphate, RNA 3'-phosphate, RNA 2'-phosphate, and DNA 3'-phosphate ends in the presence of a transition metal cofactor, which can be nickel, copper, or cobalt. HD-Pnk homologs are present in genera from 11 bacterial phyla and are often encoded in an operon with a putative ATP-dependent polynucleotide ligase. IMPORTANCE The present study provides insights regarding the diversity of nucleic acid repair strategies via the characterization of Runella slithyformis HD-Pnk as the exemplar of a novel clade of dual 5'- and 3'-end-healing enzymes that phosphorylate 5'-OH termini and dephosphorylate 2',3'-cyclic-PO4, 3'-PO4, and 2'-PO4 ends. The distinctive feature of HD-Pnk is its domain composition, i.e., a fusion of an N-terminal HD phosphohydrolase module and a C-terminal P-loop polynucleotide kinase module. Homologs of Runella HD-Pnk with the same domain composition, same domain order, and similar polypeptide sizes are distributed widely among genera from 11 bacterial phyla.
DOI: 10.1128/JB.00739-16
PubMed: 27895092
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Characterization of Runella slithyformis HD-Pnk, a Bifunctional DNA/RNA End-Healing Enzyme Composed of an N-Terminal 2',3'-Phosphoesterase HD Domain and a C-Terminal 5'-OH Polynucleotide Kinase Domain.</title><author><name sortKey="Munir, Annum" sort="Munir, Annum" uniqKey="Munir A" first="Annum" last="Munir">Annum Munir</name><affiliation wicri:level="1"><nlm:affiliation>Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Molecular Biology Program, Sloan-Kettering Institute, New York, New York</wicri:regionArea></affiliation></author><author><name sortKey="Shuman, Stewart" sort="Shuman, Stewart" uniqKey="Shuman S" first="Stewart" last="Shuman">Stewart Shuman</name><affiliation wicri:level="1"><nlm:affiliation>Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA s-shuman@ski.mskcc.org.</nlm:affiliation><country wicri:rule="url">Kiribati</country><wicri:regionArea>Molecular Biology Program, Sloan-Kettering Institute, New York, New York</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:27895092</idno><idno type="pmid">27895092</idno><idno type="doi">10.1128/JB.00739-16</idno><idno type="wicri:Area/PubMed/Corpus">000E76</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000E76</idno><idno type="wicri:Area/PubMed/Curation">000E76</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000E76</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Characterization of Runella slithyformis HD-Pnk, a Bifunctional DNA/RNA End-Healing Enzyme Composed of an N-Terminal 2',3'-Phosphoesterase HD Domain and a C-Terminal 5'-OH Polynucleotide Kinase Domain.</title><author><name sortKey="Munir, Annum" sort="Munir, Annum" uniqKey="Munir A" first="Annum" last="Munir">Annum Munir</name><affiliation wicri:level="1"><nlm:affiliation>Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Molecular Biology Program, Sloan-Kettering Institute, New York, New York</wicri:regionArea></affiliation></author><author><name sortKey="Shuman, Stewart" sort="Shuman, Stewart" uniqKey="Shuman S" first="Stewart" last="Shuman">Stewart Shuman</name><affiliation wicri:level="1"><nlm:affiliation>Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA s-shuman@ski.mskcc.org.</nlm:affiliation><country wicri:rule="url">Kiribati</country><wicri:regionArea>Molecular Biology Program, Sloan-Kettering Institute, New York, New York</wicri:regionArea></affiliation></author></analytic><series><title level="j">Journal of bacteriology</title><idno type="eISSN">1098-5530</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">5'- and 3'-end-healing reactions are key steps in nucleic acid break repair in which 5'-OH ends are phosphorylated by a polynucleotide kinase (Pnk) and 3'-PO<sub>4</sub> or 2',3'-cyclic-PO<sub>4</sub> ends are hydrolyzed by a phosphoesterase to generate the 5'-PO<sub>4</sub> and 3'-OH termini required for sealing by classic polynucleotide ligases. End-healing and sealing enzymes are present in diverse bacterial taxa, often organized as modular units within a single multifunctional polypeptide or as subunits of a repair complex. Here we identify and characterize <i>Runella slithyformis</i> HD-Pnk as a novel bifunctional end-healing enzyme composed of an N-terminal 2',3'-phosphoesterase HD domain and a C-terminal 5'-OH polynucleotide kinase P-loop domain. HD-Pnk phosphorylates 5'-OH polynucleotides (9-mers or longer) in the presence of magnesium and any nucleoside triphosphate donor. HD-Pnk dephosphorylates RNA 2',3'-cyclic phosphate, RNA 3'-phosphate, RNA 2'-phosphate, and DNA 3'-phosphate ends in the presence of a transition metal cofactor, which can be nickel, copper, or cobalt. HD-Pnk homologs are present in genera from 11 bacterial phyla and are often encoded in an operon with a putative ATP-dependent polynucleotide ligase. <b>IMPORTANCE</b> The present study provides insights regarding the diversity of nucleic acid repair strategies via the characterization of <i>Runella slithyformis</i> HD-Pnk as the exemplar of a novel clade of dual 5'- and 3'-end-healing enzymes that phosphorylate 5'-OH termini and dephosphorylate 2',3'-cyclic-PO<sub>4</sub>, 3'-PO<sub>4</sub>, and 2'-PO<sub>4</sub> ends. The distinctive feature of HD-Pnk is its domain composition, i.e., a fusion of an N-terminal HD phosphohydrolase module and a C-terminal P-loop polynucleotide kinase module. Homologs of <i>Runella</i> HD-Pnk with the same domain composition, same domain order, and similar polypeptide sizes are distributed widely among genera from 11 bacterial phyla.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27895092</PMID><DateRevised><Year>2019</Year><Month>11</Month><Day>20</Day></DateRevised><Article PubModel="Electronic-Print"><Journal><ISSN IssnType="Electronic">1098-5530</ISSN><JournalIssue CitedMedium="Internet"><Volume>199</Volume><Issue>3</Issue><PubDate><Year>2017</Year><Month>Feb</Month><Day>01</Day></PubDate></JournalIssue><Title>Journal of bacteriology</Title><ISOAbbreviation>J. Bacteriol.</ISOAbbreviation></Journal><ArticleTitle>Characterization of Runella slithyformis HD-Pnk, a Bifunctional DNA/RNA End-Healing Enzyme Composed of an N-Terminal 2',3'-Phosphoesterase HD Domain and a C-Terminal 5'-OH Polynucleotide Kinase Domain.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">e00739-16</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.1128/JB.00739-16</ELocationID><Abstract><AbstractText>5'- and 3'-end-healing reactions are key steps in nucleic acid break repair in which 5'-OH ends are phosphorylated by a polynucleotide kinase (Pnk) and 3'-PO<sub>4</sub> or 2',3'-cyclic-PO<sub>4</sub> ends are hydrolyzed by a phosphoesterase to generate the 5'-PO<sub>4</sub> and 3'-OH termini required for sealing by classic polynucleotide ligases. End-healing and sealing enzymes are present in diverse bacterial taxa, often organized as modular units within a single multifunctional polypeptide or as subunits of a repair complex. Here we identify and characterize <i>Runella slithyformis</i> HD-Pnk as a novel bifunctional end-healing enzyme composed of an N-terminal 2',3'-phosphoesterase HD domain and a C-terminal 5'-OH polynucleotide kinase P-loop domain. HD-Pnk phosphorylates 5'-OH polynucleotides (9-mers or longer) in the presence of magnesium and any nucleoside triphosphate donor. HD-Pnk dephosphorylates RNA 2',3'-cyclic phosphate, RNA 3'-phosphate, RNA 2'-phosphate, and DNA 3'-phosphate ends in the presence of a transition metal cofactor, which can be nickel, copper, or cobalt. HD-Pnk homologs are present in genera from 11 bacterial phyla and are often encoded in an operon with a putative ATP-dependent polynucleotide ligase. <b>IMPORTANCE</b> The present study provides insights regarding the diversity of nucleic acid repair strategies via the characterization of <i>Runella slithyformis</i> HD-Pnk as the exemplar of a novel clade of dual 5'- and 3'-end-healing enzymes that phosphorylate 5'-OH termini and dephosphorylate 2',3'-cyclic-PO<sub>4</sub>, 3'-PO<sub>4</sub>, and 2'-PO<sub>4</sub> ends. The distinctive feature of HD-Pnk is its domain composition, i.e., a fusion of an N-terminal HD phosphohydrolase module and a C-terminal P-loop polynucleotide kinase module. Homologs of <i>Runella</i> HD-Pnk with the same domain composition, same domain order, and similar polypeptide sizes are distributed widely among genera from 11 bacterial phyla.</AbstractText><CopyrightInformation>Copyright © 2017 American Society for Microbiology.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Munir</LastName><ForeName>Annum</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shuman</LastName><ForeName>Stewart</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA s-shuman@ski.mskcc.org.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P30 CA008748</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01 GM046330</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R37 GM046330</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>01</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Bacteriol</MedlineTA><NlmUniqueID>2985120R</NlmUniqueID><ISSNLinking>0021-9193</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">3′ phosphatase</Keyword><Keyword MajorTopicYN="N">nucleic acid repair</Keyword><Keyword MajorTopicYN="N">polynucleotide kinase</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate 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