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Catalytic Site Atlas

CSA LITERATURE entry for 1f7u

E.C. namearginine---tRNA ligase
SpeciesSaccharomyces cerevisiae (Baker's yeast)
E.C. Number (IntEnz) 6.1.1.19
CSA Homologues of 1f7u
CSA Entries With UniProtID Q05506
CSA Entries With EC Number 6.1.1.19
PDBe Entry 1f7u
PDBSum Entry 1f7u
MACiE Entry M0235

Literature Report

IntroductionArginyl-tRNA synthetase (ArgRS), isolated from Saccharomyces cerevisiae, catalyses the esterification of arginine to the 3'-terminal adenosine of a tRNA molecule. The reaction proceeds via an aminoacyl-adenylate intermediate and is ATP dependent. While the tRNA molecule is not directly involved in the formation of this intermediate, the tRNA must be bound to the enzyme before the reaction can occur. This may be due to conformational changes induced in the enzyme upon binding tRNA, as suggested for other aminoacyl-tRNA synthetases. ArgRS is a class 1a aminoacyl-tRNA synthease based on its structure, or class 1c when considering its requirement of tRNA.
MechansimThe carboxylate oxygen of arginine is the nucleophile for in-line attack on the alpha-phosphate of ATP. The transition state is trigonal bipyramidal and is stabilised by interactions with Lys156, His159, His162 and a magnesium ion (latter not found in crystal structures). The hydroxyl group of the 3'-terminal adenosine of tRNA is the nucleophile for attack on the ester of the resulting arginyl-adenylate, forming a tetrahedral intermediate. The intermediate collapses and eliminates AMP to form arginyl-tRNA.
Reaction

Catalytic Sites for 1f7u

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
LysA156156macie:sideChainLys156 forms a salt bridge with one of the non-bridging oxygens of the alpha-phosphate of ATP. This stabilises the transition states of aminoacylation, in particular the formation of the arginyl-adenylate intermediate.
HisA162162macie:sideChainHis162 interacts with the ATP phosphates and so helps to stabilise the transition state for the formation of the arginyl-adenylate intermediate.
HisA159159macie:sideChainHis159 interacts with the alpha-phosphate of ATP and helps to stabilise the transition state for the formation of the arginyl-adenylate intermediate. It is part of the conserved HIGH motif.

Literature References

Notes:
Delagoutte B
tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
EMBO J 2000 19 5599-5610
PubMed: 11060012
Cavarelli J
L-arginine recognition by yeast arginyl-tRNA synthetase.
EMBO J 1998 17 5438-5448
PubMed: 9736621
Sekine S
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.
EMBO J 2003 22 676-688
PubMed: 12554668
Airas RK.
Analysis of the kinetic mechanism of arginyl-tRNA synthetase.
Biochim Biophys Acta 2006 1764 307-319
PubMed: 16427818
Sekine S
Crucial role of the high-loop lysine for the catalytic activity of arginyl-tRNA synthetase.
J Biol Chem 2001 276 3723-3726
PubMed: 11106639
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