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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Methionine-tRNA ligaseA519Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: metG, metS, Rv1007c, MTCI237.24
EC: 6.1.1.10
UniProt
Find proteins for P9WFU5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFU5 
Go to UniProtKB:  P9WFU5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFU5
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

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Ligand Structure Quality Assessment 


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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