6JKI

Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure and catalytic mechanism of the essential m1G37 tRNA methyltransferase TrmD fromPseudomonas aeruginosa.

Jaroensuk, J.Wong, Y.H.Zhong, W.Liew, C.W.Maenpuen, S.Sahili, A.E.Atichartpongkul, S.Chionh, Y.H.Nah, Q.Thongdee, N.McBee, M.E.Prestwich, E.G.DeMott, M.S.Chaiyen, P.Mongkolsuk, S.Dedon, P.C.Lescar, J.Fuangthong, M.

(2019) Rna 25: 1481-1496

  • DOI: 10.1261/rna.066746.118
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The tRNA (m <sup>1 </sup>G37) methyltransferase TrmD catalyzes m <sup>1 </sup>G formation at position 37 in many tRNA isoacceptors and is essential in most bacteria, which positions it as a target for antibiotic development. In spite of its crucial r ...

    The tRNA (m 1 G37) methyltransferase TrmD catalyzes m 1 G formation at position 37 in many tRNA isoacceptors and is essential in most bacteria, which positions it as a target for antibiotic development. In spite of its crucial role, little is known about TrmD in Pseudomonas aeruginosa ( Pa TrmD), an important human pathogen. Here we present detailed structural, substrate and kinetic properties of Pa TrmD. Mass spectrometric analysis confirmed the G36G37-containing tRNAs Leu(GAG), Leu(CAG), Leu(UAG), Pro(GGG), Pro(UGG), Pro(CGG), and His(GUG) as Pa TrmD substrates. Analysis of steady-state kinetics with S-adenosyl-L-methionine (SAM) and tRNA Leu(GAG) showed that Pa TrmD catalyzes the two-substrate reaction by way of a ternary-complex, while isothermal titration calorimetry revealed that SAM and tRNA Leu(GAG) bind to Pa TrmD independently, each with a dissociation constant of 14 ± 3 µM. Inhibition by the SAM analog sinefungin was competitive with respect to SAM ( K i = 0.41 ± 0.07 µM) and uncompetitive for tRNA ( K i = 6.4 ± 0.8 µM). A set of crystal structures of the homodimeric Pa TrmD protein bound to SAM and sinefungin provide the molecular basis for enzyme competitive inhibition and identify the location of the bound divalent ion. These results provide insights into Pa TrmD as a potential target for the development of antibiotics.


    Organizational Affiliation

    Nanyang Technological University.,MIT.,Burapha University.,Vidyasirimedhi Institute of Science and Technology.,Nanyang Technological University, Singapore.,Chulabhorn Research Institute.,Chulabhorn Research Institute; mayuree@cri.or.th.,Massachusetts Institute of Technology.,Chulabhorn Graduate Institute.,Singapore-MIT Alliance for Research and Technology Infectious Disease IRG.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA (guanine-N(1)-)-methyltransferase
A, B
250Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: trmD
EC: 2.1.1.228
Find proteins for Q9HXQ1 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9HXQ1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SFG
Query on SFG

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Download CCD File 
A
SINEFUNGIN
ADENOSYL-ORNITHINE
C15 H23 N7 O5
LMXOHSDXUQEUSF-YECHIGJVSA-N
 Ligand Interaction
PEG
Query on PEG

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B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.670α = 90.00
b = 85.670β = 90.00
c = 147.600γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references
  • Version 1.2: 2019-10-30
    Type: Data collection, Database references