Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.53 kDa 
• Atom Count: 4027 
• Residue Count: 478 
• Unique protein chains: 1

5WYQ

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

• DOI: 10.2210/pdb5WYQ/pdb

• Classification: TRANSFERASE
• Organism(s): Pseudomonas aeruginosa UCBPP-PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-01-15 Released: 2017-12-20 
• Deposition Author(s): Jaroensuk, J., Liew, C.W., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Zhong, W., McBee, M.E., Maenpuen, S., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M., Chaiyen, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.249 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 

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., Lescar, J., Fuangthong, M.

(2019) RNA 

• PubMed: 31399541 
• DOI: 10.1261/rna.066746.118
• Primary Citation of Related Structures:  
  6JKI, 5WYR, 5WYQ


• PubMed Abstract: 
  

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. The 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.

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Organizational Affiliation: 

Center of Excellence on Environmental Health and Toxicology (EHT), Bangkok 10400, Thailand.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	248	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0  Gene Names: trmD, PA14_15990 EC: 2.1.1.228
Find proteins for Q02RL6 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore Q02RL6  Go to UniProtKB:  Q02RL6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	A, B	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.249 
• R-Value Work: 0.207 
• R-Value Observed: 0.209 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.896	α = 90
b = 85.896	β = 90
c = 147.838	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-01-15 
• Released Date: 2017-12-20 
Deposition Author(s): Jaroensuk, J., Liew, C.W., Atichartpongkul, S., Chionh, Y.H., Wong, Y.H., Zhong, W., McBee, M.E., Maenpuen, S., Prestwich, E.G., DeMott, M.S., Mongkolsuk, S., Dedon, P.C., Lescar, J., Fuangthong, M., Chaiyen, P.

Revision History 

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 1.2: 2019-10-02
  Changes: Data collection, Database references