563
Views
0
CrossRef citations to date
0
Altmetric
Research Paper

Structure and function of the pseudouridine 5’-monophosphate glycosylase PUMY from Arabidopsis thaliana

, ORCID Icon & ORCID Icon
Pages 1-10 | Accepted 05 Dec 2023, Published online: 20 Dec 2023

References

  • Frye M, Harada BT, Behm M, et al. RNA modifications modulate gene expression during development. Science. 2018;361(6409):1346–1349. doi: 10.1126/science.aau1646
  • Roundtree IA, Evans ME, Pan T, et al. Dynamic RNA modifications in gene expression regulation. Cell. 2017;169(7):1187–1200. doi: 10.1016/j.cell.2017.05.045
  • Zaccara S, Ries RJ, Jaffrey SR. Reading, writing and erasing mRNA methylation. Nat Rev Mol Cell Biol. 2019;20(10):608–624. doi: 10.1038/s41580-019-0168-5
  • Breitman TR. Pseudouridulate synthetase of Escherichia coli: correlation of its activity with utilization of pseudouridine for growth. J Bacteriol. 1970;103:263–264. doi: 10.1128/jb.103.1.263-264.1970
  • Preumont A, Snoussi K, Stroobant V, et al. Molecular identification of pseudouridine-metabolizing enzymes. J Biol Chem. 2008;283(37):25238–25246. doi: 10.1074/jbc.M804122200
  • Chen M, Witte CP. A kinase and a glycosylase catabolize pseudouridine in the peroxisome to prevent toxic pseudouridine monophosphate accumulation. Plant Cell. 2020;32(3):722–739. doi: 10.1105/tpc.19.00639
  • Thapa K, Oja T, Metsä-Ketelä M. Molecular evolution of the bacterial pseudouridine-5’-phosphate glycosidase protein family. FEBS J. 2014;281:4439–4449. doi: 10.1111/febs.12950
  • Kim SH, Witte CP, Rhee S. Structural basis for the substrate specificity and catalytic features of pseudouridine kinase from Arabidopsis thaliana. Nucleic Acids Res. 2021;49(1):491–503. doi: 10.1093/nar/gkaa1144
  • Kim SH, Kim M, Park D, et al. Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI. J Biol Chem. 2022;298(5):101869. doi: 10.1016/j.jbc.2022.101869
  • Pfeiffer M, Nidetzky B. Reverse C-glycosidase reaction provides C-nucleotide building blocks of xenobiotic nucleic acids. Nat Commun. 2020;11(1):6270. doi: 10.1038/s41467-020-20035-0
  • Huang S, Mahanta N, Begley TP, et al. Pseudouridine monophosphate glycosidase: a new glycosidase mechanism. Biochemistry. 2012;51(45):9245–9255. doi: 10.1021/bi3006829
  • Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol. 2007;372(3):774–797. doi: 10.1016/j.jmb.2007.05.022
  • Lee H, Rhee S. Structural and mutational analyses of the bifunctional arginine dihydrolase and ornithine cyclodeaminase AgrE from the cyanobacterium anabaena. J Biol Chem. 2020;295(17):5751–5760. doi: 10.1074/jbc.RA120.012768
  • Zhuang N, Zhang H, Li L, et al. Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggest a “bond-rotation” catalytic mechanism. J Biol Chem. 2020;295:2113–2124. doi: 10.1074/jbc.RA119.011752
  • Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–326.
  • Diederichs K, Karplus PA. Better models by discarding data? Acta Crystallogr D Biol Crystallogr. 2013;69(7):1215–1222. doi: 10.1107/S0907444913001121
  • Karplus PA, Diederichs K. Linking crystallographic model and data quality. Science. 2012;336(6084):1030–1033. doi: 10.1126/science.1218231
  • Liebschner D, Afonine PV, Baker ML, et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol. 2019;75(10):861–877. doi: 10.1107/S2059798319011471
  • Emsley P, Lohkamp B, Scott WG, et al. Features and development of coot. Acta Crystallogr D Biol Crystallogr. 2010;66(4):486–501. doi: 10.1107/S0907444910007493
  • Robert X, Gouet P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 2014;42(W1):W320–W324. doi: 10.1093/nar/gku316