Crystal structure of the ligand-binding form of nanoRNase from Bacteroides fragilis, a member of the DHH/DHHA1 phosphoesterase family of proteins

FEBS Lett. 2013 Aug 19;587(16):2669-74. doi: 10.1016/j.febslet.2013.06.053. Epub 2013 Jul 9.


NanoRNase (Nrn) specifically degrades nucleoside 3',5'-bisphosphate and the very short RNA, nanoRNA, during the final step of mRNA degradation. The crystal structure of Nrn in complex with a reaction product GMP was determined. The overall structure consists of two domains that are interconnected by a flexible loop and form a cleft. Two Mn²⁺ ions are coordinated by conserved residues in the DHH motif of the N-terminal domain. GMP binds near the DHHA1 motif region in the C-terminal domain. Our structure enables us to predict the substrate-bound form of Nrn as well as other DHH/DHHA1 phosphoesterase family proteins.

Keywords: Crystal structure; DHH/DHHA1 family; Nrn; RecJ exonuclease of T. thermophilus HB8; adenosine 3′,5′-bisphosphate; bfNrn; guanosine 3′,5′-bisphosphate; mRNA degradation; nanoRNA; nanoRNase; nanoRNase of Bacteroides fragilis; nanoRNase of Staphylococcus haemolyticus; nanoRNase of Thermus thermophilus HB8; pAp; pGp; shNrn; ttNrn; ttRecJ.

MeSH terms

  • Amino Acid Motifs
  • Bacterial Proteins / chemistry*
  • Bacteroides / enzymology*
  • Binding Sites
  • Crystallography, X-Ray
  • Escherichia coli / metabolism
  • Ligands
  • Manganese / chemistry
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • RNA / chemistry
  • RNA, Messenger / metabolism
  • Ribonucleases / chemistry*
  • Substrate Specificity


  • Bacterial Proteins
  • Ligands
  • RNA, Messenger
  • Manganese
  • RNA
  • Ribonucleases
  • nanoRNase, Bacteroides fragilis

Associated data

  • PDB/3W5W