NMR-based solution structure of the Caulobacter crescentus ProXp-ala trans-editing enzyme

IF 0.8 4区 生物学 Q4 BIOPHYSICS Biomolecular NMR Assignments Pub Date : 2024-08-31 DOI:10.1007/s12104-024-10193-3
Antonia D. Duran, Eric M. Danhart, Xiao Ma, Alexandra B. Kuzmishin Nagy, Karin Musier-Forsyth, Mark P. Foster
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Abstract

ProXp-ala is a key component of the translational machinery in all three Domains of life. This enzyme helps to maintain the fidelity of proline codon translation through aminoacyl-tRNAPro proofreading. In the first step of tRNA aminoacylation, the cognate aminoacyl-tRNA synthetase (aaRS) binds and activates an amino acid in the enzyme’s synthetic active site. If a non-cognate amino acid passes this first selection step and is charged onto the tRNA, a distinct aaRS editing active site may recognize the mischarged tRNA and deacylate it. Alternatively, this editing reaction may be carried out by a separate enzyme that deacylates the mischarged tRNA in trans. ProXp-ala is responsible for editing Ala mischarged onto tRNAPro. Since trans-editing domains such as ProXp-ala bind their substrates after release from the synthetase, they must recognize not only the mischarged amino acid, but also the specific tRNA. Previous studies showed that Caulobacter crescentus (Cc) ProXp-ala distinguishes tRNAPro from tRNAAla, in part, based on the unique tRNAPro acceptor stem base pair C1:G72. Previous crystallographic and NMR data also revealed a role for conformational selection by the ProXp-ala α2 helix in Ala- versus Pro-tRNAPro substrate discrimination. The α2 helix makes lattice contacts in the crystal, which left some uncertainty as to its position in solution. We report resonance assignments for the substrate-free Cc ProXp-ala and the NMR-derived three-dimensional structure of the protein. These data reveal the position of the α2 helix in solution, with implications for substrate binding and recognition.

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基于核磁共振的新月杆菌 ProXp-ala 反式编辑酶溶液结构。
ProXp-ala 是生命三大领域中翻译机制的关键组成部分。这种酶通过氨基酰-tRNAAPro 校对,帮助保持脯氨酸密码子翻译的准确性。在 tRNA 氨基酰化的第一步,同源的氨基酰-tRNA 合成酶(aaRS)在酶的合成活性位点结合并激活一个氨基酸。如果一个非认知氨基酸通过了这第一个选择步骤,并带电到 tRNA 上,一个不同的 aaRS 编辑活性位点可能会识别出带电错误的 tRNA 并使其脱酰。或者,这种编辑反应也可以由另一种酶来完成,它可以反式地使带错电的 tRNA 脱乙酰基。ProXp-ala 负责将 Ala 误充到 tRNAPro 上。由于 ProXp-ala 等反式编辑结构域从合成酶中释放出来后会与底物结合,因此它们不仅必须识别带错电荷的氨基酸,还必须识别特定的 tRNA。以前的研究表明,新月杆菌(Cc)ProXp-ala 能将 tRNAPro 与 tRNAAla 区分开来,部分原因在于 tRNAPro 独特的受体茎碱基对 C1:G72。以前的晶体学和核磁共振数据还显示,ProXp-ala α2螺旋在Ala-与Pro-tRNAPro底物的鉴别中起着构象选择的作用。α2 螺旋在晶体中具有晶格接触,因此其在溶液中的位置存在一定的不确定性。我们报告了无底物 Cc ProXp-ala 的共振分配和该蛋白质的核磁共振衍生三维结构。这些数据揭示了 α2 螺旋在溶液中的位置,并对底物结合和识别产生了影响。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Biomolecular NMR Assignments
Biomolecular NMR Assignments 生物-光谱学
CiteScore
1.70
自引率
11.10%
发文量
59
审稿时长
6-12 weeks
期刊介绍: Biomolecular NMR Assignments provides a forum for publishing sequence-specific resonance assignments for proteins and nucleic acids as Assignment Notes. Chemical shifts for NMR-active nuclei in macromolecules contain detailed information on molecular conformation and properties. Publication of resonance assignments in Biomolecular NMR Assignments ensures that these data are deposited into a public database at BioMagResBank (BMRB; http://www.bmrb.wisc.edu/), where they are available to other researchers. Coverage includes proteins and nucleic acids; Assignment Notes are processed for rapid online publication and are published in biannual online editions in June and December.
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