Abstract
α-N terminal methylation is an ubiquitous post-translational modification that is conserved throughout prokaryotes and eukaryotes. ScNTM1 is an α-N terminal methyltransferase from Saccharomyces cerevisiae that methylate ribosomal proteins i.e., Rpl12ab and Rps25a/Rps25b. Here, the crystal structures of ternary complex of ScNTM1 with its cofactor S-adenosyl-L-homocysteine (SAH) and Rps25a-based hexapeptide [PPKQQL] at 1.0 Å and binary complex of ScNTM1 with SAH at the resolution of 1.1 Å are reported. The structure revealed that ScNTM1 adopts folding similar to the known structure of the members of NTM1 subfamily and the surface displayed the evolution-related variety. Comparative structure analysis of the ternary complex of ScNTM1with the human NRMT1 and NRMT2 demonstrated that most residues participating in substrate binding are conserved. The side chain of Tyr32 plays a key role to recognize the P2 and Q4 of the hexapeptide, which is further verified by point mutation and isothermal titration calorimetry (ITC) experiments in vitro. Structural alignment of the ternary and binary complexes indicates a slight shift occurring in some regions i.e., residues (25–36, 183–186, and 215–221) upon peptide binding. The work provides structural insights into the substrate recognition of ScNTM1.
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REFERENCES
D. Han, M. Huang, T. Wang, et al., Cell Death Dis. 10, 4 (2019).
C. Dong, Y. Mao, W. Tempel, et al., Genes Dev. 29, 22 (2015).
C. Dong, G. Dong, L. Li, et al., Commun Biol. 1 (2018).
K. M. Sathyan, D. Fachinetti, and D. R. Foltz, Nat Commun. 8, (2017).
X. Dai, K. Otake, C. You, et al., J. Proteome Res. 12, 9 (2013).
Y. Kimura, Y. Kurata, A. Ishikawa, et al., Proteomics 13, 21 (2013).
A. Villar-Garea, I. Forne, I. Vetter, et al., Nucleic Acids Res. 40, 4 (2012).
R. Huang, Chembiochem 20, 8 (2019).
K. J. Webb, R. S. Lipson, Q. Al-Hadid, et al., Biochemistry 49, 25 (2010).
R. Wu, Y. Yue, X. Zheng, et al., Genes Dev. 29, 22 (2015).
S. L. Richardson, Y. Mao, G. Zhang, et al., J. Biol. Chem. 290, 18 (2015).
Z. Otwinowski and W. Minor, Methods Enzymol. 276 (1997).
P. D. Adams, P. V. Afonine, G. Bunkoczi, et al., Acta Crystallogr. D. 66, Pt 2 (2010).
P. Emsley and K. Cowtan, Acta Crystallogr. D. 60, Pt 12, Pt 1 (2004).
R. A. Laskowski and M. B. Swindells, J. Chem. Inf. Model. 51, 10 (2011).
ACKNOWLEDGMENTS
We would appreciate Dr. Muhammad Hidayatullah Khan and Dr. Wei He for assistance with critical comments and manuscript revision. We thank the staff at beamline BL17U1 and BL18U1 of the Shanghai Synchrotron Radiation Facility for help with data collection.
Funding
This work was supported by National Natural Science Foundation of China (31621002 to L.N., U1632124 to L.N., and 31270770 to Z.Z.); Ministry of Science and Technology of China (2017YFA0504903 to L.N.); Hefei National Science Center Pilot Project Funds (in part). Funding for open access charge: National Natural Science Foundation of China (31621002 to L.N.) Ministry of Science and Technology of China (2017YFA0504903 to L.N.); Hefei National Science Center Pilot Project Funds (in part).
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Haiyan Zhang performed the experiments, analyzed data and wrote paper; Zhiling Kuang and Lu Xue provided advice for the experimental process; Jian Yue provided some interpretation during the experiments; Muhammad Hidayatullah Khan modified the article; Zhongliang Zhu and Liwen Niu supervised the project. All authors read and approved the final manuscript.
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Zhang, H., Kuang, Z., Xue, L. et al. Structural Basis for Peptide Binding of α-N Terminal Methyltransferase from Saccharomyces cerevisiae. Crystallogr. Rep. 66, 1316–1321 (2021). https://doi.org/10.1134/S1063774521070257
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DOI: https://doi.org/10.1134/S1063774521070257