Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 120.50 kDa 
• Atom Count: 9079 
• Modelled Residue Count: 991 
• Deposited Residue Count: 1070 
• Unique protein chains: 1

5XGQ

Crystal structure of apo form (free-state) Mycobacterium tuberculosis methionyl-tRNA synthetase

• PDB DOI: 10.2210/pdb5XGQ/pdb

• Classification: LIGASE
• Organism(s): Mycobacterium tuberculosis H37Ra
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-15 Released: 2018-07-11 
• Deposition Author(s): Wang, W., Wang, M., Wojdyla, J.A., Cui, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.237 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 

Literature

Structural characterization of free-state and product-stateMycobacterium tuberculosismethionyl-tRNA synthetase reveals an induced-fit ligand-recognition mechanism

Wang, W., Qin, B., Wojdyla, J.A., Wang, M., Gao, X., Cui, S.

(2018) IUCrJ 5: 478-490

• PubMed: 30002848 
• DOI: 10.1107/S2052252518008217
• Primary Citation of Related Structures:  
  5XET, 5XGQ


• PubMed Abstract: 
  

Mycobacterium tuberculosis (MTB) caused 10.4 million cases of tuberculosis and 1.7 million deaths in 2016. The incidence of multidrug-resistant and extensively drug-resistant MTB is becoming an increasing threat to public health and the development of novel anti-MTB drugs is urgently needed. Methionyl-tRNA synthetase (MetRS) is considered to be a valuable drug target. However, structural characterization of M. tuberculosis MetRS (MtMetRS) was lacking for decades, thus hampering drug design. Here, two high-resolution crystal structures of MtMetRS are reported: the free-state structure (apo form; 1.9 Å resolution) and a structure with the intermediate product methionyl-adenylate (Met-AMP) bound (2.4 Å resolution). It was found that free-state MtMetRS adopts a previously unseen conformation that has never been observed in other MetRS homologues. The pockets for methionine and AMP are not formed in free-state MtMetRS, suggesting that it is in a nonproductive conformation. Combining these findings suggests that MtMetRS employs an induced-fit mechanism in ligand binding. By comparison with the structure of human cytosolic MetRS, additional pockets specific to MtMetRS that could be used for anti-MTB drug design were located.

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Organizational Affiliation: 

MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Science, No. 9 Dong Dan San Tiao, Dong Cheng Qu, Beijing 100730, People's Republic of China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine-tRNA ligase	B [auth A], A [auth B]	535	Mycobacterium tuberculosis H37Ra	Mutation(s): 0  Gene Names: metG, MRA_1016 EC: 6.1.1.10
UniProt
Find proteins for A5U150 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)) Explore A5U150  Go to UniProtKB:  A5U150

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.237 
• R-Value Work: 0.202 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.983	α = 98.9
b = 72.727	β = 90.05
c = 78.376	γ = 98.47

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-04-15 
• Released Date: 2018-07-11 
Deposition Author(s): Wang, W., Wang, M., Wojdyla, J.A., Cui, S.

Revision History  

• Version 1.0: 2018-07-11
  Type: Initial release
  
• Version 1.1: 2018-08-01
  Changes: Data collection, Database references