title: Effect of inorganic pyrophosphate on the pretransfer proofreading in the isoleucyl-tRNA synthetase from Escherichia coli.
abstract: A total rate equation was used to calculate the discrimination of valine by the isoleucyl-tRNA synthetase from Escherichia coli. The PPi present in the cell makes the backward reaction or the pyrophosphorolysis of the E.aa-AMP possible. If the E.Ile-AMP has been corrected for wrong aminoacyl adenylation by the pretransfer proofreading, the pyrophosphorolysis rapidly equilibrates the corrected E.Ile-AMP with E.Ile and thus spoils the effect of the proofreading. The loss of the corrected species is avoided if there is a barrier (perhaps conformational) formed by a slow reaction step between the noncorrected E.Ile-AMP and the corrected (*E)tRNA(Ile-AMP). If such a slow conformational change exists, the increase in accuracy from the pretransfer proofreading would be beneficial, and, in addition, the PPi increases the accuracy by optimizing the initial discrimination of the wrong amino acid.
authors.affiliation: Department of Biochemistry, University of Turku, Finland.
authors.forename: R K
authors.initials: RK
authors.lastname: Airas
mesh_terms: D000249:Adenosine Monophosphate / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology*; D007532:Isoleucine / Q000378:metabolism; D007533:Isoleucine-tRNA Ligase / Q000737:chemistry / Q000378:metabolism*; D007700:Kinetics; D010710:Phosphates / Q000494:pharmacology*; D011487:Protein Conformation; D012355:RNA, Transfer, Ile / Q000378:metabolism; D014633:Valine / Q000378:metabolism
chemical_list: D010710:Phosphates; D012355:RNA, Transfer, Ile; D007532:Isoleucine; D000249:Adenosine Monophosphate; D000255:Adenosine Triphosphate; D007533:Isoleucine-tRNA Ligase; D014633:Valine