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)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 61.56 kDa 
• Atom Count: 4077 
• Residue Count: 479 
• Unique protein chains: 1

6JOE

Crystal structure of TrmD from Pseudomonas aeruginosa in complex with active-site inhibitor

• DOI: 10.2210/pdb6JOE/pdb

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


• Deposited: 2019-03-20 Released: 2019-09-04 
• Deposition Author(s): Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.
• Funding Organization(s): National Research Foundation (Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.245 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 

Literature

Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.

Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.H., Nah, Q., Gadi, V., Gnanakalai, S., Chionh, Y.H., McBee, M.E., Gopal, P., Lim, S.H., Olivier, N., Buurman, E.T., Dick, T., Liu, C.F., Lescar, J., Dedon, P.C.

(2019) J Med Chem 62: 7788-7805

• PubMed: 31442049 
• DOI: 10.1021/acs.jmedchem.9b00582
• Primary Citation of Related Structures:  
  5ZHL, 5ZHK, 5ZHN, 5ZHM, 5ZHJ, 5ZHI, 6JOF, 6JOE


• PubMed Abstract: 
  

Among the >120 modified ribonucleosides in the prokaryotic epitranscriptome, many tRNA modifications are critical to bacterial survival, which makes their synthetic enzymes ideal targets for antibiotic development. Here we performed a structure-based design of inhibitors of tRNA-(N ¹ G37) methyltransferase, TrmD, which is an essential enzyme in many bacterial pathogens. On the basis of crystal structures of TrmDs from Pseudomonas aeruginosa and Mycobacterium tuberculosis , we synthesized a series of thienopyrimidinone derivatives with nanomolar potency against TrmD in vitro and discovered a novel active site conformational change triggered by inhibitor binding. This tyrosine-flipping mechanism is uniquely found in P. aeruginosa TrmD and renders the enzyme inaccessible to the cofactor S -adenosyl-l-methionine (SAM) and probably to the substrate tRNA. Biophysical and biochemical structure-activity relationship studies provided insights into the mechanisms underlying the potency of thienopyrimidinones as TrmD inhibitors, with several derivatives found to be active against Gram-positive and mycobacterial pathogens. These results lay a foundation for further development of TrmD inhibitors as antimicrobial agents.

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Organizational Affiliation: 

Department of Biological Engineering , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine-N(1)-)-methyltransferase	A, B	269	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	B	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
BWR	A	~{N}-[[4-[(4-azanylpiperidin-1-yl)methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2,3-d]pyrimidine-5-carboxamide C20 H23 N5 O2 S ONQHIHGODGGUGU-UHFFFAOYSA-N
PO4	A	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BWR	Kd:  91   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 0.245 
• R-Value Work: 0.209 
• R-Value Observed: 0.211 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.505	α = 90
b = 85.505	β = 90
c = 147.539	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-20 
• Released Date: 2019-09-04 
Deposition Author(s): Zhong, W., Pasunooti, K.K., Balamkundu, S., Wong, Y.W., Nah, Q., Liu, C.F., Lescar, J., Dedon, P.C.

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Funding Organization	Location	Grant Number
National Research Foundation (Singapore)	Singapore	--

Revision History 

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-09-25
  Changes: Data collection, Database references