Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d

Chin Yu Chen, Tzu Ping Ko, Ting Wan Lin, Chia Cheng Chou, Chun Jung Chen, Andrew H.J. Wang

Research output: Contribution to journalArticlepeer-review

25 Citations (Scopus)


Sac7d, a small abundant sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (∼60°) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant-DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (∼50°). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (∼ 80°). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower Tm values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA.

Original languageEnglish
Pages (from-to)430-438
Number of pages9
JournalNucleic Acids Research
Issue number1
Publication statusPublished - 2005
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d'. Together they form a unique fingerprint.

Cite this