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Nucleic Acids Research Advance Access originally published online on November 25, 2008
Nucleic Acids Research 2009 37(1):193-203; doi:10.1093/nar/gkn928
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Nucleic Acids Research, 2009, Vol. 37, No. 1 193-203
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Nucleic Acid Enzymes

Involvement of the TPR2 subdomain movement in the activities of {phi}29 DNA polymerase

Irene Rodríguez, José María Lázaro, Margarita Salas* and Miguel de Vega

Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C/Nicolás Cabrera 1, Cantoblanco, 28049 Madrid, Spain

*To whom correspondence should be addressed. Tel: +34 911964675/4402; Fax: +34 911964677; Email: msalas{at}cbm.uam.es

Received September 22, 2008. Revised November 3, 2008. Accepted November 3, 2008.

The polymerization domain of {phi}29 DNA polymerase acquires a toroidal shape by means of an arch-like structure formed by the specific insertion TPR2 (Terminal Protein Region 2) and the thumb subdomain. TPR2 is connected to the fingers and palm subdomains through flexible regions, suggesting that it can undergo conformational changes. To examine whether such changes take place, we have constructed a {phi}29 DNA polymerase mutant able to form a disulfide bond between the apexes of TPR2 and thumb to limit the mobility of TPR2. Biochemical analysis of the mutant led us to conclude that TPR2 moves away from the thumb to allow the DNA polymerase to replicate circular ssDNA. Despite the fact that no TPR2 motion is needed to allow the polymerase to use the terminal protein (TP) as primer during the initiation of {phi}29 TP–DNA replication, the disulfide bond prevents the DNA polymerase from entering the elongation phase, suggesting that TPR2 movements are necessary to allow the TP priming domain to move out from the polymerase during transition from initiation to elongation. Furthermore, the TPR2-thumb bond does not affect the equilibrium between the polymerization and exonuclease activities, leading us to propose a primer-terminus transference model between both active sites.

Present address: Irene Rodríguez, Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), C/Arturo Duperier, 4, 28029 Madrid, Spain


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