Structural basis for tRNA-dependent amidotransferase function

Emmanuelle Schmitt; Michel Panvert; Sylvain Blanquet; Yves Mechulam

doi:10.1016/j.str.2005.06.016

Structural basis for tRNA-dependent amidotransferase function

Structure. 2005 Oct;13(10):1421-33. doi: 10.1016/j.str.2005.06.016.

Authors

Emmanuelle Schmitt¹, Michel Panvert, Sylvain Blanquet, Yves Mechulam

Affiliation

¹ Laboratoire de Biochimie, Unité Mixte de Recherche 7654, CNRS-Ecole Polytechnique, F-91128 Palaiseau cedex, France. emma@botrytis.polytechnique.fr

PMID: 16216574
DOI: 10.1016/j.str.2005.06.016

Abstract

Besides direct charging of tRNAs by aminoacyl-tRNA synthetases, indirect routes also ensure attachment of some amino acids onto tRNA. Such routes may explain how new amino acids entered into protein synthesis. In archaea and in most bacteria, tRNA(Gln) is first misaminoacylated by glutamyl-tRNA synthetase. Glu-tRNA(Gln) is then matured into Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. We report the structure of a tRNA-dependent amidotransferase-that of GatDE from Pyrococcus abyssi. The 3.0 A resolution crystal structure shows a tetramer with two GatD molecules as the core and two GatE molecules at the periphery. The fold of GatE cannot be related to that of any tRNA binding enzyme. The ammonium donor site on GatD and the tRNA site on GatE are markedly distant. Comparison of GatD and L-asparaginase structures shows how the motion of a beta hairpin region containing a crucial catalytic threonine may control the overall reaction cycle of GatDE.

MeSH terms

Amino Acid Sequence
Amino Acyl-tRNA Synthetases / chemistry
Amino Acyl-tRNA Synthetases / metabolism
Binding Sites
Conserved Sequence
Crystallography, X-Ray
Dimerization
Glutamate-tRNA Ligase / chemistry
Glutamate-tRNA Ligase / metabolism
Models, Molecular
Molecular Sequence Data
Nitrogenous Group Transferases / chemistry*
Nitrogenous Group Transferases / genetics
Nitrogenous Group Transferases / metabolism*
Protein Biosynthesis
Protein Folding
Protein Structure, Secondary
Protein Structure, Tertiary
Protein Subunits / chemistry
Pyrococcus abyssi / enzymology
RNA, Archaeal / chemistry*
RNA, Archaeal / genetics
RNA, Archaeal / metabolism*
RNA, Bacterial / chemistry
RNA, Bacterial / genetics
RNA, Bacterial / metabolism
RNA, Transfer / chemistry*
RNA, Transfer / metabolism*
RNA, Transfer, Gln / metabolism
Sequence Homology, Amino Acid
Threonine / chemistry
X-Ray Diffraction

Substances

Protein Subunits
RNA, Archaeal
RNA, Bacterial
RNA, Transfer, Gln
Threonine
RNA, Transfer
Nitrogenous Group Transferases
Amino Acyl-tRNA Synthetases
Glutamate-tRNA Ligase

Associated data

PDB/1ZQ1