Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase

Bernstein, N. K.; Hammel, M.; Mani, R. S.; Weinfeld, M.; Pelikan, M.; Tainer, J. A.; Glover, J. N.  M.

doi:10.1093/nar/gkp597

Title: Mechanism of DNA substrate recognition by the mammalian DNA repair enzyme, Polynucleotide Kinase

Journal Article · 11 August 2009 · Nucleic Acids Research

DOI: https://doi.org/10.1093/nar/gkp597 · OSTI ID:1625464

Bernstein, N. K. ^[1]; Hammel, M. ^[2]; Mani, R. S. ^[3]; Weinfeld, M. ^[3]; Pelikan, M. ^[4]; Tainer, J. A. ^[5]; Glover, J. N. M. ^[6]

Univ. of Alberta, Edmonton, AB (Canada). Dept. of Biochemistry; DOE/OSTI
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division
Cross Cancer Inst., Edmonton, AB (Canada). Dept. of Experimental Oncology
Univ. of Missouri, St. Louis, MO (United States). Dept. of Mathematics and Computer Science
The Scripps Research Inst., La Jolla, CA (United States). Skaggs Inst. of Chemical Biology. Dept. of Molecular Biology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Life Sciences Division. Dept. of Molecualr Biology
Univ. of Alberta, Edmonton, AB (Canada). Dept. of Biochemistry

Mammalian polynucleotide kinase (mPNK) is a critical DNA repair enzyme whose 5’-kinase and 3’-phoshatase activities function with poorly understood but striking specificity to restore 5’- phosphate/3’-hydroxyl termini at sites of DNA damage. Here we integrated site-directed mutagenesis and small-angle X-ray scattering (SAXS) combined with advanced computational approaches to characterize the conformational variability and DNA-binding properties of mPNK. The flexible attachment of the FHA domain to the catalytic segment, elucidated by SAXS, enables the interactions of mPNK with diverse DNA substrates and protein partners required for effective orchestration of DNA end repair. Point mutations surrounding the kinase active site identified two substrate recognition surfaces positioned to contact distinct regions on either side of the phosphorylated 5’-hydroxyl. DNA substrates bind across the kinase active site cleft to position the double-stranded portion upstream of the 5’-hydroxyl on one side, and the 3’-overhang on the opposite side. The bipartite DNA-binding surface of the mPNK kinase domain explains its preference for recessed 5’-termini, structures that would be encountered in the course of DNA strand break repair.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625464

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 18 Vol. 37; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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