5GMB

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruiginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.

Jaroensuk, J.Atichartpongkul, S.Chionh, Y.H.Wong, Y.H.Liew, C.W.McBee, M.E.Thongdee, N.Prestwich, E.G.DeMott, M.S.Mongkolsuk, S.Dedon, P.C.Lescar, J.Fuangthong, M.

(2016) Nucleic Acids Res 44: 10834-10848

  • DOI: 10.1093/nar/gkw870
  • Primary Citation of Related Structures:  
    5GM8, 5GMC, 5GMB

  • PubMed Abstract: 
  • Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress ...

    Bacteria respond to environmental stresses using a variety of signaling and gene expression pathways, with translational mechanisms being the least well understood. Here, we identified a tRNA methyltransferase in Pseudomonas aeruginosa PA14, trmJ, which confers resistance to oxidative stress. Analysis of tRNA from a trmJ mutant revealed that TrmJ catalyzes formation of Cm, Um, and, unexpectedly, Am. Defined in vitro analyses revealed that tRNA Met(CAU) and tRNA Trp(CCA) are substrates for Cm formation, tRNA Gln(UUG) , tRNA Pro(UGG) , tRNA Pro(CGG) and tRNA His(GUG) for Um, and tRNA Pro(GGG) for Am. tRNA Ser(UGA) , previously observed as a TrmJ substrate in Escherichia coli, was not modified by PA14 TrmJ. Position 32 was confirmed as the TrmJ target for Am in tRNA Pro(GGG) and Um in tRNA Gln(UUG) by mass spectrometric analysis. Crystal structures of the free catalytic N-terminal domain of TrmJ show a 2-fold symmetrical dimer with an active site located at the interface between the monomers and a flexible basic loop positioned to bind tRNA, with conformational changes upon binding of the SAM-analog sinefungin. The loss of TrmJ rendered PA14 sensitive to H 2 O 2 exposure, with reduced expression of oxyR-recG, katB-ankB, and katE These results reveal that TrmJ is a tRNA:Cm32/Um32/Am32 methyltransferase involved in translational fidelity and the oxidative stress response.


    Organizational Affiliation

    Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok, Thailand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJA171Pseudomonas aeruginosaMutation(s): 0 
Gene Names: 
EC: 2.1.1.200
UniProt
Find proteins for A0A072ZPM2 (Pseudomonas aeruginosa)
Explore A0A072ZPM2 
Go to UniProtKB:  A0A072ZPM2
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.796α = 90
b = 59.796β = 90
c = 124.18γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references, Derived calculations