Biomaterial Database

Catalytic mechanism of valyl-tRNA synthetase from baker's yeast. Reaction pathway and rate-determining step in the aminoacylation of tRNAVal. 1981

D Kern, and J Gangloff

The catalytic mechanism of valyl-tRNA synthetase from baker's yeast has been investigated by pre-steady-state and steady-state kinetic measurements and end product dissociation studies. The pre-steady-state kinetics show a lag period during the early time when the reaction is started with free enzyme. The preincubation of the synthetase with tRNAVal and/or valine or preformation of Val approximately AMP leads to a progressive suppression of the lag. This lag probably reflects conformational transitions of the enzyme-substrate complex necessary for the transfer. At low pH or at a low ionic strength, the tRNAVal charging occurs much faster at the pre steady state than at the steady state. We show that after the fast transfer of valine from adenylate to tRNAVal, followed by the fast dissociation of AMP and PPi, a new adenylate is synthesized which promotes the dissociation of the nascent Val-tRNAVal. This dissociation occurs in a multistep process. First ATP and magnesium promote the ejection of the valine moiety of Val-tRNAVal from the adenylate site. A new adenylate is then synthesized which promotes, in the presence of magnesium, several state changes of the end product complex. A complex is finally generated in which the enzyme-bound Val-tRNAVal is able to exchange rapidly with a tRNAVal molecule. The free tRNAVal plays an active role in this exchange. Depending upon the experimental conditions, one of these steps can determine the steady-state rate of tRNAVal charging. The dissociations of enzyme-bound uncharged tRNAVal or aa-tRNAs substituted on the amino acid or on the tRNA parts by noncognate parts as well as the effect of the replacement of the adenylates by wrong adenylates have been investigated. It is shown that the valine and the tRNA moieties of Val-tRNAVal and the valine moiety of the adenylate are involved in this mechanism of dissociation. Finally, the rate-determining step of the reversal of tRNAVal charging at the steady-state has been investigated. It is shown that this step is the dissociation of the deacylated tRNAVal from enzyme.

UI	MeSH Term	Description	Entries
D007700	Kinetics	The rate dynamics in chemical or physical systems.
D008274	Magnesium	A metallic element that has the atomic symbol Mg, atomic number 12, and atomic weight 24.31. It is important for the activity of many enzymes, especially those involved in OXIDATIVE PHOSPHORYLATION.
D000215	Acylation	The addition of an organic acid radical into a molecule.
D000604	Amino Acyl-tRNA Synthetases	A subclass of enzymes that aminoacylate AMINO ACID-SPECIFIC TRANSFER RNA with their corresponding AMINO ACIDS.	Amino Acyl T RNA Synthetases,Amino Acyl-tRNA Ligases,Aminoacyl Transfer RNA Synthetase,Aminoacyl-tRNA Synthetase,Transfer RNA Synthetase,tRNA Synthetase,Acyl-tRNA Ligases, Amino,Acyl-tRNA Synthetases, Amino,Amino Acyl tRNA Ligases,Amino Acyl tRNA Synthetases,Aminoacyl tRNA Synthetase,Ligases, Amino Acyl-tRNA,RNA Synthetase, Transfer,Synthetase, Aminoacyl-tRNA,Synthetase, Transfer RNA,Synthetase, tRNA,Synthetases, Amino Acyl-tRNA
D012343	RNA, Transfer	The small RNA molecules, 73-80 nucleotides long, that function during translation (TRANSLATION, GENETIC) to align AMINO ACIDS at the RIBOSOMES in a sequence determined by the mRNA (RNA, MESSENGER). There are about 30 different transfer RNAs. Each recognizes a specific CODON set on the mRNA through its own ANTICODON and as aminoacyl tRNAs (RNA, TRANSFER, AMINO ACYL), each carries a specific amino acid to the ribosome to add to the elongating peptide chains.	Suppressor Transfer RNA,Transfer RNA,tRNA,RNA, Transfer, Suppressor,Transfer RNA, Suppressor,RNA, Suppressor Transfer
D012441	Saccharomyces cerevisiae	A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.	Baker's Yeast,Brewer's Yeast,Candida robusta,S. cerevisiae,Saccharomyces capensis,Saccharomyces italicus,Saccharomyces oviformis,Saccharomyces uvarum var. melibiosus,Yeast, Baker's,Yeast, Brewer's,Baker Yeast,S cerevisiae,Baker's Yeasts,Yeast, Baker
D014637	Valine-tRNA Ligase	An enzyme that activates valine with its specific transfer RNA. EC 6.1.1.9	Valyl T RNA Synthetase,Val-tRNA Ligase,Valyl-tRNA Synthetase,Ligase, Val-tRNA,Ligase, Valine-tRNA,Synthetase, Valyl-tRNA,Val tRNA Ligase,Valine tRNA Ligase,Valyl tRNA Synthetase
D015636	Magnesium Chloride	Magnesium chloride. An inorganic compound consisting of one magnesium and two chloride ions. The compound is used in medicine as a source of magnesium ions, which are essential for many cellular activities. It has also been used as a cathartic and in alloys.	MgCl2,Chloride, Magnesium
D046249	Transfer RNA Aminoacylation	The conversion of uncharged TRANSFER RNA to AMINO ACYL TRNA.	Aminoacylation, Transfer RNA,Transfer RNA Charging,tRNA Aminoacylation,tRNA Charging,Amino Acid Activation, Translational,Transfer RNA Acylation,Transfer RNA Amino Acylation,tRNA Acylation,tRNA Amino Acylation,Acylation, Transfer RNA,Acylation, tRNA,Acylations, Transfer RNA,Acylations, tRNA,Amino Acylation, tRNA,Aminoacylation, tRNA,Aminoacylations, Transfer RNA,Aminoacylations, tRNA,RNA Aminoacylations, Transfer,RNA Charging, Transfer,Transfer RNA Acylations,Transfer RNA Aminoacylations,Transfer RNA Chargings,tRNA Acylations,tRNA Aminoacylations,tRNA Chargings