August 31, 2016 Journal article Closed Access

Marco De Vivo; Marco De Vivo; Emiliano Ippoliti; Vito Genna; Vito Genna; Paolo Carloni; Pietro Vidossich

DataCite XML Export

<?xml version='1.0' encoding='utf-8'?>
<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4.1/metadata.xsd">
  <identifier identifierType="URL">https://www.openaccessrepository.it/record/91731</identifier>
  <creators>
    <creator>
      <creatorName>Marco De Vivo</creatorName>
    </creator>
    <creator>
      <creatorName>Marco De Vivo</creatorName>
    </creator>
    <creator>
      <creatorName>Emiliano Ippoliti</creatorName>
    </creator>
    <creator>
      <creatorName>Vito Genna</creatorName>
    </creator>
    <creator>
      <creatorName>Vito Genna</creatorName>
    </creator>
    <creator>
      <creatorName>Paolo Carloni</creatorName>
    </creator>
    <creator>
      <creatorName>Pietro Vidossich</creatorName>
    </creator>
  </creators>
  <titles>
    <title>A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases</title>
  </titles>
  <publisher>INFN Open Access Repository</publisher>
  <publicationYear>2016</publicationYear>
  <subjects>
    <subject>Colloid and Surface Chemistry</subject>
    <subject>Biochemistry</subject>
    <subject>General Chemistry</subject>
    <subject>Catalysis</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2016-08-31</date>
  </dates>
  <language>en</language>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://www.openaccessrepository.it/record/91731</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1021/jacs.6b05475</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://www.openaccessrepository.it/communities/itmirror</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="info:eu-repo/semantics/closedAccess">Closed Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">The enzymatic polymerization of DNA and RNA is the basis for genetic inheritance for all living organisms. It is catalyzed by the DNA/RNA polymerase (Pol) superfamily. Here, bioinformatics analysis reveals that the incoming nucleotide substrate always forms an H-bond between its 3′-OH and β-phosphate moieties upon formation of the Michaelis complex. This previously unrecognized H-bond implies a novel self-activated mechanism (SAM), which synergistically connects the in situ nucleophile formation with subsequent nucleotide addition and, importantly, nucleic acid translocation. Thus, SAM allows an elegant and efficient closed-loop sequence of chemical and physical steps for Pol catalysis. This is markedly different from previous mechanistic hypotheses. Our proposed mechanism is corroborated via ab initio QM/MM simulations on a specific Pol, the human DNA polymerase-η, an enzyme involved in repairing damaged DNA. The structural conservation of DNA and RNA Pols supports the possible extension of SAM to Pol enzymes from the three domains of life.</description>
  </descriptions>
</resource>