Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

Structure. 2005 Jul;13(7):973-84. doi: 10.1016/j.str.2005.04.015.

Abstract

RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Catalytic Domain
  • Chromatography
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Endoribonucleases / chemistry
  • Escherichia coli / enzymology*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry
  • Hydrogen Bonding
  • Ions
  • Models, Molecular
  • Molecular Conformation
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Conformation
  • Protein Structure, Tertiary
  • Proteins / chemistry
  • RNA / chemistry
  • RNA, Bacterial
  • Ribonuclease III / chemistry*
  • Sequence Homology, Amino Acid
  • Substrate Specificity

Substances

  • Escherichia coli Proteins
  • Ions
  • Proteins
  • RNA, Bacterial
  • RNA
  • Endoribonucleases
  • Ribonuclease III

Associated data

  • PDB/1YT3