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Structure of a bifunctional DNA primase-polymerase

Nature Structural & Molecular Biology volume 11, pages 157162 (2004) | Download Citation

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Abstract

Genome replication generally requires primases, which synthesize an initial oligonucleotide primer, and DNA polymerases, which elongate the primer. Primase and DNA polymerase activities are combined, however, in newly identified replicases from archaeal plasmids, such as pRN1 from Sulfolobus islandicus. Here we present a structure-function analysis of the pRN1 primase-polymerase (prim-pol) domain. The crystal structure shows a central depression lined by conserved residues. Mutations on one side of the depression reduce DNA affinity. On the opposite side of the depression cluster three acidic residues and a histidine, which are required for primase and DNA polymerase activity. One acidic residue binds a manganese ion, suggestive of a metal-dependent catalytic mechanism. The structure does not show any similarity to DNA polymerases, but is distantly related to archaeal and eukaryotic primases, with corresponding active-site residues. We propose that archaeal and eukaryotic primases and the prim-pol domain have a common evolutionary ancestor, a bifunctional replicase for small DNA genomes.

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Acknowledgements

We thank A. Schmidt for excellent technical assistance, K. Zeth for data collection at ESRF, and C. Schulze-Briese and the staff of beamline X06SA of the Swiss Light Source for help. P.C. is supported by the Deutsche Forschungsgemeinschaft, the EMBO Young Investigator Programme and the Fonds der chemischen Industrie. G.L. is supported by the Deutsche Forschungsgemeinschaft. G.L. dedicates this work to G. Krauss, University of Bayreuth, on the occasion of his 60th birthday.

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  1. Institute of Biochemistry, University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany.

    • Georg Lipps
    •  & Gudrun von Scheven
  2. Institute of Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Strasse 25, D-81377 Munich, Germany.

    • Andreas O Weinzierl
    • , Claudia Buchen
    •  & Patrick Cramer

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The authors declare no competing financial interests.

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Correspondence to Georg Lipps or Patrick Cramer.

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https://doi.org/10.1038/nsmb723

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