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Nucleic Acids Research Advance Access published online on November 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp955
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© The Author(s) 2009. Published by Oxford University Press.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition

Akiyoshi Nakamura1, Kelly Sheppard2, Junji Yamane1, Min Yao1,3, Dieter Söll2,4 and Isao Tanaka1,3,*

1Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan, 2Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA, 3Faculty of Advanced Life Science, Hokkaido University, kita-10, nishi-8, Sapporo, Hokkaido, 060-0810, Japan and 4Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA

*To whom correspondence should be addressed. Tel/Fax: +81 11 706 3221; Email: tanaka{at}castor.sci.hokudai.ac.jp

Received September 1, 2009. Revised October 6, 2009. Accepted October 10, 2009.

In many prokaryotes the biosynthesis of the amide aminoacyl-tRNAs, Gln-tRNAGln and Asn-tRNAAsn, proceeds by an indirect route in which mischarged Glu-tRNAGln or Asp-tRNAAsn 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:tRNAGln 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-tRNAAsn from Asp-tRNAAsp in archaea. Furthermore, we identified a 310 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.


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