Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition

Nucleic Acids Res. 2010 Jan;38(2):672-82. doi: 10.1093/nar/gkp955. Epub 2009 Nov 11.

Abstract

In many prokaryotes the biosynthesis of the amide aminoacyl-tRNAs, Gln-tRNA(Gln) and Asn-tRNA(Asn), proceeds by an indirect route in which mischarged Glu-tRNA(Gln) or Asp-tRNA(Asn) is amidated to the correct aminoacyl-tRNA catalyzed by a tRNA-dependent amidotransferase (AdT). Two types of AdTs exist: bacteria, archaea and organelles possess heterotrimeric GatCAB, while heterodimeric GatDE occurs exclusively in archaea. Bacterial GatCAB and GatDE recognize the first base pair of the acceptor stem and the D-loop of their tRNA substrates, while archaeal GatCAB recognizes the tertiary core of the tRNA, but not the first base pair. Here, we present the crystal structure of the full-length Staphylococcus aureus GatCAB. Its GatB tail domain possesses a conserved Lys rich motif that is situated close to the variable loop in a GatCAB:tRNA(Gln) docking model. This motif is also conserved in the tail domain of archaeal GatCAB, suggesting this basic region may recognize the tRNA variable loop to discriminate Asp-tRNA(Asn) from Asp-tRNA(Asp) in archaea. Furthermore, we identified a 3(10) turn in GatB that permits the bacterial GatCAB to distinguish a U1-A72 base pair from a G1-C72 pair; the absence of this element in archaeal GatCAB enables the latter enzyme to recognize aminoacyl-tRNAs with G1-C72 base pairs.

Publication types

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

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry*
  • Base Pairing
  • Crystallography, X-Ray
  • Models, Molecular
  • Molecular Sequence Data
  • Nitrogenous Group Transferases / chemistry*
  • Protein Structure, Tertiary
  • RNA, Transfer / chemistry*
  • RNA, Transfer, Asn / chemistry
  • RNA, Transfer, Gln / chemistry
  • Staphylococcus aureus / enzymology*

Substances

  • Bacterial Proteins
  • RNA, Transfer, Asn
  • RNA, Transfer, Gln
  • RNA, Transfer
  • Nitrogenous Group Transferases

Associated data

  • PDB/3IP4