NMR structure determination of the Escherichia coli DnaJ molecular chaperone: secondary structure and backbone fold of the N-terminal region (residues 2-108) containing the highly conserved J domain

Proc Natl Acad Sci U S A. 1994 Nov 22;91(24):11343-7. doi: 10.1073/pnas.91.24.11343.

Abstract

DnaJ from Escherichia coli is a 376-amino acid protein that functions in conjunction with DnaK and GrpE as a chaperone machine. The N-terminal fragment of residues 2-108, DnaJ-(2-108), retains many of the activities of the full-length protein and contains a structural motif, the J domain of residues 2-72, which is highly conserved in a superfamily of proteins. In this paper, NMR spectroscopy was used to determine the secondary structure and the three-dimensional polypeptide backbone fold of DnaJ-(2-108). By using 13C/15N doubly labeled DnaJ-(2-108), nearly complete sequence-specific assignments were obtained for 1H, 15N, 13C alpha, and 13C beta, and about 40% of the peripheral aliphatic carbon resonances were also assigned. Four alpha-helices in polypeptide segments of residues 6-11, 18-31, 41-55, and 61-68 in the J domain were identified by sequential and medium-range nuclear Overhauser effects. For the J domain, the three-dimensional structure was calculated with the program DIANA from an input of 536 nuclear Overhauser effect upper-distance constraints and 52 spin-spin coupling constants. The polypeptide backbone fold is characterized by the formation of an antiparallel bundle of two long helices, residues 18-31 and 41-55, which is stabilized by a hydrophobic core of side chains that are highly conserved in homologous J domain sequences. The Gly/Phe-rich region from residues 77 to 108 is flexibly disordered in solution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Escherichia coli / chemistry
  • Escherichia coli Proteins
  • HSP40 Heat-Shock Proteins
  • Heat-Shock Proteins / ultrastructure*
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Chaperones / ultrastructure*
  • Molecular Sequence Data
  • Protein Structure, Secondary
  • Protein Structure, Tertiary

Substances

  • DnaJ protein, E coli
  • Escherichia coli Proteins
  • HSP40 Heat-Shock Proteins
  • Heat-Shock Proteins
  • Molecular Chaperones