NMR structure of ribonuclease HI from Escherichia coli

Masako Fujiwara, Toshiyo Kato, Toshio Yamazaki, Kazuhiko Yamasaki, Kuniaki Nagayama

Research output: Contribution to journalArticlepeer-review

9 Citations (Scopus)


The solution structure of ribonuclease HI (RNase HI) from Escherichia coli (E. coli), a protein of 155 residues, was determined. Three-dimensional nuclear Overhauser enhancement spectroscopy (NOESY) was used to obtain 1424 distance constraints between individually assigned polypeptide chain hydrogen atoms. Supplemental geometric constraints of 90φ angles and 12χ 1 angles, and the distance constraints of 66 hydrogen bonds were experimentally derived. Using the DADAS90 program that calculates structures in dihedral angle space, 15 structures satisfying almost all constraints were obtained. The average root mean square deviation (RMSD) from the mean structure was 0.75 Å for backbone atoms. The RMSD for backbone atoms between the representative NMR structure with the smallest constraint violation and crystal structures was within 1.2 Å. Although the NMR and crystal structures thus resemble one another, a significant discrepancy was observed in a region termed 'basic protrusion.' The discrepancy observed in NMR experiments is explained by fluctuation in this region.

Original languageEnglish
Pages (from-to)1147-1152
Number of pages6
JournalBiological and Pharmaceutical Bulletin
Issue number10
Publication statusPublished - 2000


  • Distance geometry
  • NOE
  • Ribonuclease H
  • Solution structure

ASJC Scopus subject areas

  • Molecular Medicine
  • Pharmacology, Toxicology and Pharmaceutics(all)


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