The solution structure of the DNA double-stranded break repair protein Ku and its complex with DNA: A neutron contrast variation study

Jinkui Zhao, Jinting Wang, David J. Chen, Scott R. Peterson, Jill Trewhella

Research output: Contribution to journalArticle

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Abstract

Small-angle X-ray and neutron scattering with contrast variation has been used to study the structure of the DNA targeting component (Ku) of the DNA-dependent protein kinase and its complex with DNA. The Ku protein in solution has the approximate shape of a prolate ellipsoid with semi-axes of 24, 43, and 89 Å. In the presence of a minimal-length DNA binding sequence (a 24-base-pair duplex DNA), a 1:1 Ku/DNA complex forms. This 1:1 stoichiometry is observed when either the Ku or the DNA is in excess. Analysis of the contrast variation data on Ku complexed with either the 24- mer duplex DNA or a slightly longer 30-mer duplex DNA shows that both the DNA and Ku structures have the same overall conformations within the 1:1 complex as the uncomplexed components. The separation of the centers-of-mass for the Ku/24-mer DNA complex is 46 Å, while that for the Ku/30-mer DNA is 56 Å. The DNA binds within what appears to be a preformed channel that penetrates deeply into the Ku protein such that the entire length of the 24-mer DNA spans the protein. The slightly longer 30-mer binds in a similar fashion, but with its extra length protruding from the protein envelop. The scattering data are consistent with the idea that the Ku 'threads' onto the duplex DNA via a channel that can completely bury approximately 24 base pairs.

Original languageEnglish (US)
Pages (from-to)2152-2159
Number of pages8
JournalBiochemistry
Volume38
Issue number7
DOIs
StatePublished - Feb 16 1999

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Double-Stranded DNA Breaks
Neutrons
Repair
DNA
Proteins
Base Pairing
Ku Autoantigen
Phosmet
DNA-Activated Protein Kinase
Neutron scattering
X ray scattering
Stoichiometry
Conformations

ASJC Scopus subject areas

  • Biochemistry

Cite this

The solution structure of the DNA double-stranded break repair protein Ku and its complex with DNA : A neutron contrast variation study. / Zhao, Jinkui; Wang, Jinting; Chen, David J.; Peterson, Scott R.; Trewhella, Jill.

In: Biochemistry, Vol. 38, No. 7, 16.02.1999, p. 2152-2159.

Research output: Contribution to journalArticle

Zhao, Jinkui ; Wang, Jinting ; Chen, David J. ; Peterson, Scott R. ; Trewhella, Jill. / The solution structure of the DNA double-stranded break repair protein Ku and its complex with DNA : A neutron contrast variation study. In: Biochemistry. 1999 ; Vol. 38, No. 7. pp. 2152-2159.
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