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Nucleic Acids Research 2005 33(13):4172-4181; doi:10.1093/nar/gki736
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Published online 25 July 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen

Chin-Ju Park, Joon-Hwa Lee and Byong-Seok Choi*

Department of Chemistry, National Creative Research Initiative Center, Korea Advanced Institute of Science and Technology 373-1, Guseong-dong, Yuseong-gu, Daejon 305-701, Korea

*To whom correspondence should be addressed at Department of Chemistry, Center for Repair System of Damaged DNA, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejon 305-701 Korea. Tel: +82 42 869 2828; Fax: +82 42 869 2810; Email: byongseok.choi{at}kaist.ac.kr

Received April 13, 2005. Revised June 23, 2005. Accepted July 9, 2005.

Replication protein A (RPA) is a three-subunit complex with multiple roles in DNA metabolism. DNA-binding domain A in the large subunit of human RPA (hRPA70A) binds to single-stranded DNA (ssDNA) and is responsible for the species-specific RPA–T antigen (T-ag) interaction required for Simian virus 40 replication. Although Saccharomyces cerevisiae RPA70A (scRPA70A) shares high sequence homology with hRPA70A, the two are not functionally equivalent. To elucidate the similarities and differences between these two homologous proteins, we determined the solution structure of scRPA70A, which closely resembled the structure of hRPA70A. The structure of ssDNA-bound scRPA70A, as simulated by residual dipolar coupling-based homology modeling, suggested that the positioning of the ssDNA is the same for scRPA70A and hRPA70A, although the conformational changes that occur in the two proteins upon ssDNA binding are not identical. NMR titrations of hRPA70A with T-ag showed that the T-ag binding surface is separate from the ssDNA-binding region and is more neutral than the corresponding part of scRPA70A. These differences might account for the species-specific nature of the hRPA70A–T-ag interaction. Our results provide insight into how these two homologous RPA proteins can exhibit functional differences, but still both retain their ability to bind ssDNA.

Present address: Joon-Hwa Lee, Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA

The authors wish it to be known that, in their opinion, the first two authors should be regarded as First Authors

PDB no. 1YNX


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E. Fanning, V. Klimovich, and A. R. Nager
A dynamic model for replication protein A (RPA) function in DNA processing pathways
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[Abstract] [Full Text] [PDF]


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