6AX8

Mycobacterium tuberculosis methionyl-tRNA synthetase in complex with methionyl-adenylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The crystal structure of the drug target Mycobacterium tuberculosis methionyl-tRNA synthetase in complex with a catalytic intermediate.

Barros-Alvarez, X.Turley, S.Ranade, R.M.Gillespie, J.R.Duster, N.A.Verlinde, C.L.M.J.Fan, E.Buckner, F.S.Hol, W.G.J.

(2018) Acta Crystallogr F Struct Biol Commun 74: 245-254

  • DOI: 10.1107/S2053230X18003151
  • Primary Citation of Related Structures:  
    6AX8

  • PubMed Abstract: 
  • Mycobacterium tuberculosis is a pathogenic bacterial infectious agent that is responsible for approximately 1.5 million human deaths annually. Current treatment requires the long-term administration of multiple medicines with substantial side effects. Lack of compliance, together with other factors, has resulted in a worrisome increase in resistance ...

    Mycobacterium tuberculosis is a pathogenic bacterial infectious agent that is responsible for approximately 1.5 million human deaths annually. Current treatment requires the long-term administration of multiple medicines with substantial side effects. Lack of compliance, together with other factors, has resulted in a worrisome increase in resistance. New treatment options are therefore urgently needed. Here, the crystal structure of methionyl-tRNA synthetase (MetRS), an enzyme critical for protein biosynthesis and therefore a drug target, in complex with its catalytic intermediate methionyl adenylate is reported. Phenylalanine 292 of the M. tuberculosis enzyme is in an `out' conformation and barely contacts the adenine ring, in contrast to other MetRS structures where ring stacking occurs between the adenine and a protein side-chain ring in the `in' conformation. A comparison with human cytosolic MetRS reveals substantial differences in the active site as well as regarding the position of the connective peptide subdomain 1 (CP1) near the active site, which bodes well for arriving at selective inhibitors. Comparison with the human mitochondrial enzyme at the amino-acid sequence level suggests that arriving at inhibitors with higher affinity for the mycobacterial enzyme than for the mitochondrial enzyme might be achievable.


    Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine-tRNA ligaseA519Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: metGmetSRv1007cMTCI237.24
EC: 6.1.1.10
UniProt
Find proteins for P9WFU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFU5 
Go to UniProtKB:  P9WFU5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ME8 (Subject of Investigation/LOI)
Query on ME8

Download Ideal Coordinates CCD File 
B [auth A][[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] (2S)-2-azanyl-4-methylsulfanyl-butanoate
C15 H23 N6 O8 P S
RZQLXQQLNKBFRX-TWBCTODHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.237 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 196.958α = 90
b = 196.958β = 90
c = 39.177γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1 AI084004 and RO1 AI097177

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence