Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (317K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (7)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Eastberg, J. H.
Right arrow Articles by Stoddard, B. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Eastberg, J. H.
Right arrow Articles by Stoddard, B. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 30 January 2004

Nucleic Acids Research, 2004, Vol. 32, No. 2 653-660
© 2004 Oxford University Press

Recognition of DNA substrates by T4 bacteriophage polynucleotide kinase

Jennifer H. Eastberg, John Pelletier1 and Barry L. Stoddard*

Fred Hutchinson Cancer Research Center and the Graduate Program in Molecular and Cellular Biology, University of Washington, 1100 Fairview Avenue North, A3-025, Seattle, WA 98109, USA and 1 New England Biolabs, 32 Tozer Road, Beverly, MA 01915, USA

*To whom correspondence should be addressed. Tel: +1 206 667 4031; Fax: +1 206 667 5894; Email: bstoddar{at}fhcrc.org

T4 phage polynucleotide kinase (PNK) displays 5'-hydroxyl kinase, 3'-phosphatase and 2',3'-cyclic phosphodiesterase activities. The enzyme phosphorylates the 5' hydroxyl termini of a wide variety of nucleic acid substrates, a behavior studied here through the determination of a series of crystal structures with single-stranded (ss)DNA oligonucleotide substrates of various lengths and sequences. In these structures, the 5' ribose hydroxyl is buried in the kinase active site in proper alignment for phosphoryl transfer. Depending on the ssDNA length, the first two or three nucleotide bases are well ordered. Numerous contacts are made both to the phosphoribosyl backbone and to the ordered bases. The position, side chain contacts and internucleotide stacking interactions of the ordered bases are strikingly different for a 5'-GT DNA end than for a 5'-TG end. The base preferences displayed at those positions by PNK are attributable to differences in the enzyme binding interactions and in the DNA conformation for each unique substrate molecule.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
N. K. Bernstein, M. Hammel, R. S. Mani, M. Weinfeld, M. Pelikan, J. A. Tainer, and J. N. M. Glover
Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase
Nucleic Acids Res., October 1, 2009; 37(18): 6161 - 6173.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
R. Jain and S. Shuman
Characterization of a thermostable archaeal polynucleotide kinase homologous to human Clp1
RNA, May 1, 2009; 15(5): 923 - 931.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
A. Ramirez, S. Shuman, and B. Schwer
Human RNA 5'-kinase (hClp1) can function as a tRNA splicing enzyme in vivo
RNA, September 1, 2008; 14(9): 1737 - 1745.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
R. S. Mani, M. Fanta, F. Karimi-Busheri, E. Silver, C. A. Virgen, K. W. Caldecott, C. E. Cass, and M. Weinfeld
XRCC1 Stimulates Polynucleotide Kinase by Enhancing Its Damage Discrimination and Displacement from DNA Repair Intermediates
J. Biol. Chem., September 21, 2007; 282(38): 28004 - 28013.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
H. Zhu, S. Yin, and S. Shuman
Characterization of Polynucleotide Kinase/Phosphatase Enzymes from Mycobacteriophages Omega and Cjw1 and Vibriophage KVP40
J. Biol. Chem., June 18, 2004; 279(25): 26358 - 26369.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.