The hyperthermophile chromosomal protein Sac7d sharply kinks DNA - PubMed (original) (raw)

. 1998 Mar 12;392(6672):202-5.

doi: 10.1038/32455.

Affiliations

• PMID: 9515968
• DOI: 10.1038/32455

The hyperthermophile chromosomal protein Sac7d sharply kinks DNA

H Robinson et al. Nature. 1998.

Abstract

The proteins Sac7d and Sso7d belong to a class of small chromosomal proteins from the hyperthermophilic archaeon Sulfolobus acidocaldarius and S. solfactaricus, respectively. These proteins are extremely stable to heat, acid and chemical agents. Sac7d binds to DNA without any particular sequence preference and thereby increases its melting temperature by approximately 40 degrees C. We have now solved and refined the crystal structure of Sac7d in complex with two DNA sequences to high resolution. The structures are examples of a nonspecific DNA-binding protein bound to DNA, and reveal that Sac7d binds in the minor groove, causing a sharp kinking of the DNA helix that is more marked than that induced by any sequence-specific DNA-binding proteins. The kink results from the intercalation of specific hydrophobic side chains of Sac7d into the DNA structure, but without causing any significant distortion of the protein structure relative to the uncomplexed protein in solution.

PubMed Disclaimer

Similar articles

• The crystal structure of the hyperthermophile chromosomal protein Sso7d bound to DNA.
  Gao YG, Su SY, Robinson H, Padmanabhan S, Lim L, McCrary BS, Edmondson SP, Shriver JW, Wang AH. Gao YG, et al. Nat Struct Biol. 1998 Sep;5(9):782-6. doi: 10.1038/1822. Nat Struct Biol. 1998. PMID: 9731772
• Crystal structures of the chromosomal proteins Sso7d/Sac7d bound to DNA containing T-G mismatched base-pairs.
  Su S, Gao YG, Robinson H, Liaw YC, Edmondson SP, Shriver JW, Wang AH. Su S, et al. J Mol Biol. 2000 Oct 27;303(3):395-403. doi: 10.1006/jmbi.2000.4112. J Mol Biol. 2000. PMID: 11031116
• Structures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers.
  Ko TP, Chu HM, Chen CY, Chou CC, Wang AH. Ko TP, et al. Acta Crystallogr D Biol Crystallogr. 2004 Aug;60(Pt 8):1381-7. doi: 10.1107/S0907444904012065. Epub 2004 Jul 21. Acta Crystallogr D Biol Crystallogr. 2004. PMID: 15272160
• Synthetic metallopeptides as probes of protein-DNA interactions.
  Long EC, Eason PD, Liang Q. Long EC, et al. Met Ions Biol Syst. 1996;33:427-52. Met Ions Biol Syst. 1996. PMID: 8742851 Review. No abstract available.
• Intercalation, DNA kinking, and the control of transcription.
  Werner MH, Gronenborn AM, Clore GM. Werner MH, et al. Science. 1996 Feb 9;271(5250):778-84. doi: 10.1126/science.271.5250.778. Science. 1996. PMID: 8628992 Review.

Cited by

• Structural predictions of protein-DNA binding: MELD-DNA.
  Esmaeeli R, Bauzá A, Perez A. Esmaeeli R, et al. Nucleic Acids Res. 2023 Feb 28;51(4):1625-1636. doi: 10.1093/nar/gkad013. Nucleic Acids Res. 2023. PMID: 36727436 Free PMC article.
• Evaluation of docking procedures reliability in affitins-partners interactions.
  Ranaudo A, Cosentino U, Greco C, Moro G, Bonardi A, Maiocchi A, Moroni E. Ranaudo A, et al. Front Chem. 2022 Dec 1;10:1074249. doi: 10.3389/fchem.2022.1074249. eCollection 2022. Front Chem. 2022. PMID: 36531315 Free PMC article.
• Charge Engineering Improves the Performance of Bst DNA Polymerase Fusions.
  Paik I, Bhadra S, Ellington AD. Paik I, et al. ACS Synth Biol. 2022 Apr 15;11(4):1488-1496. doi: 10.1021/acssynbio.1c00559. Epub 2022 Mar 23. ACS Synth Biol. 2022. PMID: 35320674 Free PMC article.
• Lysine Methylation Modulates the Interaction of Archaeal Chromatin Protein Cren7 With DNA.
  Ding N, Chen Y, Chu Y, Zhong C, Huang L, Zhang Z. Ding N, et al. Front Microbiol. 2022 Mar 3;13:837737. doi: 10.3389/fmicb.2022.837737. eCollection 2022. Front Microbiol. 2022. PMID: 35308404 Free PMC article.
• Engineering Strategies to Overcome the Stability-Function Trade-Off in Proteins.
  Teufl M, Zajc CU, Traxlmayr MW. Teufl M, et al. ACS Synth Biol. 2022 Mar 18;11(3):1030-1039. doi: 10.1021/acssynbio.1c00512. Epub 2022 Mar 8. ACS Synth Biol. 2022. PMID: 35258287 Free PMC article. Review.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Nature Publishing Group
  • Ovid Technologies, Inc.

• Other Literature Sources

  • The Lens - Patent Citations