Asymmetric behavior of archaeal prolyl‐tRNA synthetase

Ambrogelly, Alexandre; Kamtekar, S.; Stathopoulos, Constantinos; Kennedy, Dexter; Söll, Dieter

doi:10.1016/j.febslet.2005.09.025

Cited by 15 publications

(19 citation statements)

References 28 publications

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“…Both of these class I tRNA synthetases are homodimers that catalyze (at least under some conditions), synthesis of approximately 1 mol of aminoacyl adenylate. It has also been shown that the class II M. jannaschii ProRS and E. coli HisRS homodimers rapidly synthesize only 1 mol of aminoacyl adenylate per dimer (51)(52)(53). Our data now extend the half-ofthe-sites reactivity phenomenon to also encompass a homotetrameric enzyme; thus, the phenomenon appears to be generally present in multimeric tRNA synthetases of both classes.…”

Section: Discussionmentioning

confidence: 61%

The Homotetrameric Phosphoseryl-tRNA Synthetase from Methanosarcina mazei Exhibits Half-of-the-sites Activity

Hauenstein

Hou

Perona

2008

Journal of Biological Chemistry

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Synthesis of cysteinyl-tRNACys in methanogenic archaea proceeds by a two-step pathway in which tRNA Cys is first aminoacylated with phosphoserine by phosphoseryl-tRNA synthetase (SepRS). Characterization of SepRS from the mesophile Methanosarcina mazei by gel filtration and nondenaturing mass spectrometry shows that the native enzyme exists as an ␣4 tetramer when expressed at high levels in Escherichia coli. However, active site titrations monitored by ATP/PP i burst kinetics, together with analysis of tRNA binding stoichiometry by fluorescence spectroscopy, show that the tetrameric enzyme binds two tRNAs and that only two of the four chemically equivalent subunits catalyze formation of phosphoseryl adenylate. Therefore, the phenomenon of half-of-the-sites activity, previously described for synthesis of 1 mol of tyrosyl adenylate by the dimeric class I tyrosyl-tRNA synthetase, operates as well in this homotetrameric class II tRNA synthetase. Analysis of cognate and noncognate reactions by ATP/PP i and aminoacylation kinetics strongly suggests that SepRS is able to discriminate against the noncognate amino acids glutamate, serine, and phosphothreonine without the need for a separate hydrolytic editing site. tRNA Cys binding to SepRS also enhances the capacity of the enzyme to discriminate among amino acids, indicating the existence of functional connectivity between the tRNA and amino acid binding sites of the enzyme.

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Section: Discussionmentioning

confidence: 61%

The Homotetrameric Phosphoseryl-tRNA Synthetase from Methanosarcina mazei Exhibits Half-of-the-sites Activity

Hauenstein

Hou

Perona

2008

Journal of Biological Chemistry

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“…A number of oligomeric aaRS have previously been shown to exhibit activity of half of the sites despite containing multiple, seemingly chemically equivalent active and tRNA-binding sites (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)30). The mode of tRNA binding described herein argues that SepSecS may follow the sequential model of allosteric regulation (49).…”

Section: Discussionmentioning

confidence: 86%

“…The TyrRS dimer binds one tRNA Tyr (15) and catalyzes formation of 1 mol of tyrosyl adenylate (16 -20), and tetrameric PheRS (15,21) and SepRS (22) employ two of their four catalytic and tRNA-binding sites at a time. Likewise, class II enzymes, bacterial LysRS-II (23,24), AspRS (25), and HisRS (26) and the archaeal and eukaryotic ProRS (27,28) behave according to the "half of the sites" model. The situation is less clear in the case of PylRS and SerRS.…”

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confidence: 99%

Structural Asymmetry of the Terminal Catalytic Complex in Selenocysteine Synthesis

French

Gupta

Copeland

et al. 2014

Journal of Biological Chemistry

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Background: SepSecS catalyzes the terminal step of selenocysteine synthesis in a reaction that requires tRNA Sec . Results: SepSecS simultaneously binds up to two tRNAs in a cross-dimer fashion. Conclusion:The SepSecS-tRNA Sec complex is asymmetric: one dimer is a noncatalytic platform that binds tRNAs, whereas the other one catalyzes the reaction. Significance: The study proposes allosteric regulation of selenocysteine and selenoprotein synthesis.

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“…Alternatively, the half-of-the-sites reactivity may arise during tRNA binding to a preexisting symmetric dimer to the highly interdigitating and expansive interface of the two monomers (accounting for 26% of the total surface per monomer), which may form the binding surface for the G37 base and may be constructed in such a way to allow only one tRNA to bind to one subunit or alternatively bind across the dimer interface, leading to the stoichiometry of one tRNA bound per dimer. Half-of-the-sites activity has been previously shown for dimeric and tetrameric aaRSs of both the Rossmann-fold and the non-Rossmann-fold type 17;28;29;43;44;45. The discovery of half-of-the-sites reactivity for TrmD suggests that this phenomenon may be general to multimeric enzymes that operate on tRNA.…”

Section: Discussionmentioning

confidence: 88%

Control of Catalytic Cycle by a Pair of Analogous tRNA Modification Enzymes

Christian

Lahoud

Liu

et al. 2010

Journal of Molecular Biology

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Enzymes that use distinct active site structures to perform identical reactions are known as analogous enzymes. The isolation of analogous enzymes suggests the existence of multiple enzyme structural pathways that can catalyze the same chemical reaction. A fundamental question concerning analogous enzymes is whether their distinct active-site structures would confer the same or different kinetic constraints to the chemical reaction, particularly with respect to the control of enzyme turnover. Here we address this question with the analogous enzymes of bacterial TrmD and its eukaryotic and archaeal counterpart Trm5. While both TrmD and Trm5 catalyze methyl transfer to synthesize the m1G37 base at the 3' position adjacent to the tRNA anticodon, using S-adenosyl methionine (AdoMet) as the methyl donor, TrmD features a trefoil-knot active-site structure whereas Trm5 features the Rossmann fold. Pre-steady-state analysis revealed that product synthesis by TrmD proceeds linearly with time, whereas that by Trm5 exhibits a rapid burst followed by a slower and linear increase with time. The burst kinetics of Trm5 suggests that product release is the rate-limiting step of the catalytic cycle, consistent with the observation of higher enzyme affinities to the products of tRNA and AdoMet. In contrast, the lack of burst kinetics of TrmD suggests that its turnover is controlled by a step required for product synthesis. Although TrmD exists as a homodimer, it showed "half-of-the-sites" reactivity for tRNA binding and product synthesis. The kinetic differences between TrmD and Trm5 are parallel to those between the two classes of aminoacyl-tRNA synthetases, which use distinct active-site structures to catalyze tRNA aminoacylation. This parallel suggests that the findings have a fundamental importance for enzymes that catalyze both methyl and aminoacyl transfer to tRNA in the decoding process.

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Asymmetric behavior of archaeal prolyl‐tRNA synthetase

Cited by 15 publications

References 28 publications

The Homotetrameric Phosphoseryl-tRNA Synthetase from Methanosarcina mazei Exhibits Half-of-the-sites Activity

The Homotetrameric Phosphoseryl-tRNA Synthetase from Methanosarcina mazei Exhibits Half-of-the-sites Activity

Structural Asymmetry of the Terminal Catalytic Complex in Selenocysteine Synthesis

Control of Catalytic Cycle by a Pair of Analogous tRNA Modification Enzymes

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