A peculiar property of aspartyl-tRNA synthetase from bakers' yeast: chemical modification of the protein by the enzymically synthesized aminoacyl adenylate

Kern, Daniel; Lorber, Bernard; Boulanger, Yves; Giegé, Richard

doi:10.1021/bi00327a009

Cited by 46 publications

(47 citation statements)

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“…Experiments reported here show that in the absence of the CoA acceptor, the enzyme contains a freely diffusible highly reactive intermediate, with similar properties to other highfree-energy phosphotransfer intermediates such as aminoacyl adenylates (Kern et al, 1985). This further confirms the similarity of the mechanisms of ATP-citrate lyase and succinylCoA synthetase.…”

supporting

confidence: 79%

“…Similar results are obtained with succinyl-CoA synthetase (Benson et al, 1969;Pearson and Bridger, 1975) when the enzyme is incubated with succinate and ATP but no CoA. The effect is common when an enzyme is stalled with a high-freeenergy intermediate in its active site, and has been studied in most detail for aminoacyl-tRNA synthetases in the absence of their cognate tRNA (Kern et al, 1985;Rapaport et al, 1985;Lowe et al, 1987).…”

Section: Discussionsupporting

confidence: 53%

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ATP‐citrate lyase from rat liver

Wells¹

1991

European Journal of Biochemistry

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The mechanism of ATP-citrate lyase has been proposed to involve a citryl-enzyme intermediate. When the enzyme is incubated with its substrates ATP and [14C]citrate, but in the absence of the final acceptor, two distinct types of citrate-containing complex can be isolated. At early time points, a highly unstable complex can be isolated by gel filtration which has a half-life of 36 s at 25 "C. This complex reacts rapidly with CoA, but cannot be acidprecipitated; behaviour consistent with its identification as enzyme-citryl phosphate. However, ATP-citrate lyase is also capable of undergoing a slow time-dependent covalent incorporation of radiolabel from [ 14C]citrate. This modification is acid-stable, non-specific, and cannot be reversed by the addition of CoA. When cytochrome c is included in the reaction mixture as a heterologous acceptor, it is also citrylated. These reactions require that when ATP-citrate lyase is incubated with all its substrates except for CoA, a freely diffusible citrylating species is generated within the active site. This evidence suggests that there is no requirement for the mechanism of ATPcitrate lyase to proceed via a covalent citryl-enzyme intermediate. By analogy with succinyl-CoA synthetase, an enzyme which has a high degree of sequence similarity with ATP-citrate lyase, a simple mechanism is proposed for the enzyme in which citryl-CoA is produced by direct nucleophilic attack on citryl phosphate.

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supporting

confidence: 79%

Section: Discussionsupporting

confidence: 53%

ATP‐citrate lyase from rat liver

Wells¹

1991

European Journal of Biochemistry

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“…Acquisition by AspRS of the capacity to activate this COOH group had to be accompanied by the loss of tRNA aminoacylation to prevent isopeptide bond formation in proteins and premature termination of peptide elongation on ribosomes. Further, because the activated Asp can react with nucleophilic acceptors (26), loss of the tRNA charging capacity of the ␤-COOH-activating AspRS had to be correlated with acquisition of the amidation reaction to prevent release of AspϳAMP.…”

Section: Discussionmentioning

confidence: 99%

When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism

Roy

Becker

Reinbolt

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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Faithful protein synthesis relies on a family of essential enzymes called aminoacyl-tRNA synthetases, assembled in a piecewise fashion. Analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-tRNA synthetase (AsnRS) also display a second ORF encoding an AsnRS truncated from its anticodon binding-domain (AsnRS2). We show herein that Pyrococcus abyssi AsnRS2, in contrast to AsnRS, does not sustain asparaginyl-tRNA Asn synthesis but is instead capable of converting aspartic acid into asparagine. Functional analysis and complementation of an Escherichia coli asparagine auxotrophic strain show that AsnRS2 constitutes the archaeal homologue of the bacterial ammonia-dependent asparagine synthetase A (AS-A), therefore named archaeal asparagine synthetase A (AS-AR). Primary sequence-and 3D-based phylogeny shows that an archaeal AspRS ancestor originated AS-AR, which was subsequently transferred into bacteria by lateral gene transfer in which it underwent structural changes producing AS-A. This study provides evidence that a contemporary aminoacyl-tRNA synthetase can be recruited to sustain amino acid metabolism.A ccurate protein translation requires a complete set of 20 species of perfectly paired aminoacyl-tRNAs (aa-tRNAs). It was therefore expected that each organism should possess 20 aa-tRNA synthetases (aaRSs), each capable of matching a particular amino acid (aa) to the cognate tRNA (reviewed in ref. 1). However, the vast number of sequences that emerged from genome sequencing and biochemical investigations revealed anomalies that forced a revision of this assumption (2). Archaea and various eubacteria are deprived of glutaminyl-tRNA synthetase and more exceptionally of asparaginyl-tRNA synthetase (AsnRS). The homologous aa-tRNAs are formed indirectly by amidation of Glu and Asp, respectively, mischarged on tRNA Gln and tRNA Asn by a glutamyl-tRNA synthetase (GluRS) or an aspartyl-tRNA synthetase (AspRS) of relaxed specificity (3-6). In bacteria of the Thermus͞Deinococcus group, deprived of the enzymes forming free asparagine (Asn), the indirect route to tRNA asparaginylation also constitutes the sole pathway of Asn biosynthesis (6, 7).The functional interrelation between the direct and the indirect pathways of amide aa-tRNA formation is not well understood, and the phylogenetic relationship of their partners has not been explored. Emergence of the direct pathways of tRNA glutaminylation and asparaginylation had to be accompanied by concomitant apparition of the enzymes forming the free aa and the homologous aa-tRNA. The paths leading to the emergence of glutaminyl-tRNA synthetase and AsnRS have been documented (8, 9), but the origin of the Gln-and Asn-forming enzymes remains unclear. In particular, it is not known whether the aaRS and the enzyme forming the cognate free aa originated from the same ancestor.The microbial genomes are sprinkled with polypeptide chains consisting of one of the functional domains of aaRSs (10). In some cases, the participation of these domains in a v...

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“…18,19) In the case of yeast, the possiblity of an interaction between tRNAAsP and lysine residues of AspRS was reported. 20) The interaction between the 3 '-end of tRNA and aminoacyl-tRNA synthetase was indicated on the peptide map' ) or by photo-crosslinking. 22) In this paper, we report the interaction between SerRS and the substrates (tRNAser, Ser or ATP) studied by chemical modification of SerRS, as well as some kinetic parameters of bovine SerRS for some serine tRNA species.…”

Section: Introductionmentioning

confidence: 99%

Protection of bovine seryl-transfer ribonucleic acid (seryl-tRNA) synthetase from chemical modification by its substrates, and some kinetic parameters.

Tachibana

Mizutani

1988

CHEMICAL & PHARMACEUTICAL BULLETIN

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Amino acid residues contained in the recognition sites of seryl-transfer ribonucleic acid (tRNA) synthetase (SerRS) were studied by chemical modification.Ser residues were modified with phenylmethanesulfonyl fluoride, and appeared to be unnecessary for the recognition. However, the modification of Arg residues with phenylglyoxal, His residues with diethylpyrocarbonate and sulfhydryl groups with 5,5'-dithiobis(2-nitrobenzoic acid), N-ethylmaleimide, iodoacetic acid or iodoacetamide showed that these residues were essential for the tRNA recognition by SerRS. Protection experiments with substrates from inactivation of Ser-tRNA formation by modification suggested that Arg residues interact with the y-phosphate of adenosine triphosphate and tRNA .Modification of sulfhydryl groups showed that the groups interact with the hydroxyl groups of ribose of the CCA-end on tRNA. Furthermore, in order to understand the recognition mechanism between SerRS and tRNAser, some kinetic parameters such as the Km and V. values of yeast tRNAs" and E. coli tRNAser for bovine SerRS were compared with the values of bovine tRNAser .

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A peculiar property of aspartyl-tRNA synthetase from bakers' yeast: chemical modification of the protein by the enzymically synthesized aminoacyl adenylate

Cited by 46 publications

References 38 publications

ATP‐citrate lyase from rat liver

ATP‐citrate lyase from rat liver

When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism

Protection of bovine seryl-transfer ribonucleic acid (seryl-tRNA) synthetase from chemical modification by its substrates, and some kinetic parameters.

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