1k61
MATALPHA2 HOMEODOMAIN BOUND TO DNA
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OverviewOverview
Hoogsteen base pairs within duplex DNA typically are only observed in regions containing significant distortion or near sites of drug intercalation. We report here the observation of a Hoogsteen base pair embedded within undistorted, unmodified B-DNA. The Hoogsteen base pair, consisting of a syn adenine base paired with an anti thymine base, is found in the 2.1 A resolution structure of the MATalpha2 homeodomain bound to DNA in a region where a specifically and a non-specifically bound homeodomain contact overlapping sites. NMR studies of the free DNA show no evidence of Hoogsteen base pair formation, suggesting that protein binding favors the transition from a Watson-Crick to a Hoogsteen base pair. Molecular dynamics simulations of the homeodomain-DNA complex support a role for the non-specifically bound protein in favoring Hoogsteen base pair formation. The presence of a Hoogsteen base pair in the crystal structure of a protein-DNA complex raises the possibility that Hoogsteen base pairs could occur within duplex DNA and play a hitherto unrecognized role in transcription, replication and other cellular processes.
About this StructureAbout this Structure
1K61 is a Single protein structure of sequence from [1]. Full crystallographic information is available from OCA.
ReferenceReference
A Hoogsteen base pair embedded in undistorted B-DNA., Aishima J, Gitti RK, Noah JE, Gan HH, Schlick T, Wolberger C, Nucleic Acids Res. 2002 Dec 1;30(23):5244-52. PMID:12466549
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