Backbone resonance assignment for the full length tRNA-(N1G37) methyltransferase of Pseudomonas aeruginosa

  • Yan Li
  • Wenhe Zhong
  • Ann Zhufang Koay
  • Hui Qi Ng
  • Qianhui Nah
  • Yee Hwa Wong
  • Jeffrey Hill
  • Julien LescarEmail author
  • Peter C. DedonEmail author
  • CongBao KangEmail author


Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation, making it an important target for the development of new antibacterial compounds. TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-l-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer. Here we report the backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa. Most resonances were assigned and the secondary structure for each amino acid was determined according to the assigned backbone resonances. The availability of the assignment will be valuable for exploring molecular interactions of TrmD with ligands, inhibitors and tRNA.


TrmD Pseudomonas aeruginosa tRNA methyltransferase Epitranscriptome Drug discovery Antibacterial Protein dynamics Backbone assignment 



CK appreciates the support from NMRC OF-IRG Grant (NMRC/OFIRG/0051/2017) and A*STAR JCO Grant (1431AFG102/1331A028). This work is also supported by National Research Foundation of Singapore through the Singapore-MIT-Alliance for Research and Technology (SMART) Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups. WZ was supported by a SMART Scholar Fellowship. We also thank Prof Ho Sup Yoon and Dr. Hong Ye from Nanyang Technological University for the NMR experiments. The authors appreciate the valuable discussion from the team members at EDDC, A*STAR.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.


  1. Bjork G, Wikstrom P, Bystrom A (1989) Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science 244:986–989CrossRefGoogle Scholar
  2. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293CrossRefGoogle Scholar
  3. Gayen S, Li Q, Kang C (2012) The solution structure of the S4-S5 linker of the hERG potassium channel. J Pept Sci 18:140–145CrossRefGoogle Scholar
  4. Goto-Ito S, Ito T, Kuratani M, Bessho Y, Yokoyama S (2009) Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation. Nat Struct Mol Biol 16:1109–1115CrossRefGoogle Scholar
  5. Goto-Ito S, Ito T, Yokoyama S (2017) Trm5 and TrmD: two enzymes from distinct origins catalyze the identical tRNA modification, m(1)G37. Biomolecules 7:32CrossRefGoogle Scholar
  6. Hill PJ, Abibi A, Albert R, Andrews B, Gagnon MM, Gao N, Grebe T, Hajec LI, Huang J, Livchak S, Lahiri SD, McKinney DC, Thresher J, Wang H, Olivier N, Buurman ET (2013) Selective Inhibitors of bacterial t-RNA-(N1G37) methyltransferase (TrmD) that demonstrate novel ordering of the lid domain. J Med Chem 56:7278–7288CrossRefGoogle Scholar
  7. Holmes WM, Andraos-Selim C, Redlak M (1995) tRNA-m1G methyltransferase interactions: touching bases with structure. Biochimie 77:62–65CrossRefGoogle Scholar
  8. Ito T, Masuda I, Yoshida K-I, Goto-Ito S, Sekine S-I, Suh SW, Hou Y-M, Yokoyama S (2015) Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Proc Natl Acad Sci 112:E4197–E4205CrossRefGoogle Scholar
  9. Johnson BA (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol Biol 278:313–352Google Scholar
  10. Juhling F, Morl M, Hartmann RK, Sprinzl M, Stadler PF, Putz J (2009) tRNAdb 2009: compilation of tRNA sequences and tRNA genes. Nucleic Acids Res 37:D159–D162CrossRefGoogle Scholar
  11. Kim YM, Li Q, Ng HQ, Yoon HS, Kang C (2013) 1H, 13C and 15N chemical shift assignments for the N-terminal PAS domain of the KCNH channel from Zebrafish. Biomol NMR Assign 8:165–168CrossRefGoogle Scholar
  12. Li Q, Raida M, Kang C (2010) 1H, 13C and 15N chemical shift assignments for the N-terminal domain of the voltage-gated potassium channel-hERG. Biomol NMR Assign 4:211–213CrossRefGoogle Scholar
  13. Li Y, Wong YL, Lee MY, Ng HQ, Kang C (2016) Backbone assignment of the N-terminal 24-kDa fragment of Escherichia coli topoisomerase IV ParE subunit. Biomol NMR Assign 10:135–138CrossRefGoogle Scholar
  14. Li Y, Zhong W, Koay AZ, Ng HQ, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Lescar J, Hill J, Dedon PC, Kang C (2018) Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N1G37) methyltransferase. Biomol NMR Assign 13:49–53CrossRefGoogle Scholar
  15. O’Dwyer K, Watts JM, Biswas S, Ambrad J, Barber M, Brulé H, Petit C, Holmes DJ, Zalacain M, Holmes WM (2004) Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growth. J Bacteriol 186:2346–2354CrossRefGoogle Scholar
  16. Persson BC, Bylund GO, Berg DE, Wikstrom PM (1995) Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics. J Bacteriol 177:5554–5560CrossRefGoogle Scholar
  17. Pervushin K, Ono A, Fernandez C, Szyperski T, Kainosho M, Wuthrich K (1998) NMR scalar couplings across Watson–Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc Natl Acad Sci USA 95:14147–14151CrossRefGoogle Scholar
  18. Salzmann M, Pervushin K, Wider G, Senn H, Wuthrich K (1998) TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc Natl Acad Sci USA 95:13585–13590CrossRefGoogle Scholar
  19. Shen Y, Bax A (2013) Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks. J Biomol NMR 56:227–241CrossRefGoogle Scholar
  20. Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223CrossRefGoogle Scholar
  21. Thanassi JA, Hartman-Neumann SL, Dougherty TJ, Dougherty BA, Pucci MJ (2002) Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Res 30:3152–3162CrossRefGoogle Scholar
  22. Thomas SR, Keller CA, Szyk A, Cannon JR, LaRonde-LeBlanc NA (2011) Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Nucleic Acids Res 39:2445–2457CrossRefGoogle Scholar
  23. Zhang Z, Li Y, Loh YR, Phoo WW, Hung AW, Kang C, Luo D (2016) Crystal structure of unlinked NS2B-NS3 protease from Zika virus. Science 354:1597–1600CrossRefGoogle Scholar
  24. Zhong W, Koay A, Ngo A, Li Y, Nah Q, Wong YH, Chionh YH, Ng HQ, Koh-Stenta X, Poulsen A, Foo K, McBee M, Choong ML, El Sahili A, Kang C, Matter A, Lescar J, Hill J, Dedon P (2019) Targeting the bacterial epitranscriptome for antibiotic development: discovery of novel tRNA-(N(1)G37) methyltransferase (TrmD) inhibitors. ACS Infect Dis 3:326–335CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Experimental Drug Development CentreSingaporeSingapore
  2. 2.Infectious Disease and Antimicrobial Resistance Interdisciplinary Research GroupsSingapore-MIT Alliance for Research and TechnologySingaporeSingapore
  3. 3.NTU Institute of Structural BiologyNanyang Technological UniversitySingaporeSingapore
  4. 4.School of Biological SciencesNanyang Technological UniversitySingaporeSingapore
  5. 5.Department of Biological EngineeringMassachusetts Institute of TechnologyCambridgeUSA
  6. 6.Department of Pathogen Biology, School of Basic Medicine, Tongji Medical CollegeHuazhong University of Science and TechnologyWuhanPeople’s Republic of China

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