Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 62.00 kDa 
• Atom Count: 4291 
• Modelled Residue Count: 520 
• Deposited Residue Count: 530 
• Unique protein chains: 1

7WPI

Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor

• PDB DOI: 10.2210/pdb7WPI/pdb

• Classification: LIGASE/INHIBITOR
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-24 Released: 2022-04-27 
• Deposition Author(s): Yi, J., Cai, Z., Qiu, H., Lu, F., Chen, B., Luo, Z., Gu, Q., Xu, J., Zhou, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.237 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Literature

Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase.

Yi, J., Cai, Z., Qiu, H., Lu, F., Luo, Z., Chen, B., Gu, Q., Xu, J., Zhou, H.

(2022) Nucleic Acids Res 

• PubMed: 35474479 
• DOI: 10.1093/nar/gkac285
• Primary Citation of Related Structures:  
  7WPI, 7WPJ, 7WPK, 7WPL, 7WPM, 7WPN, 7WPT, 7WPX, 7WQ0


• PubMed Abstract: 
  

Methionyl-tRNA synthetase (MetRS) charges tRNAMet with l-methionine (L-Met) to decode the ATG codon for protein translation, making it indispensable for all cellular lives. Many gram-positive bacteria use a type 1 MetRS (MetRS1), which is considered a promising antimicrobial drug target due to its low sequence identity with human cytosolic MetRS (HcMetRS, which belongs to MetRS2). Here, we report crystal structures of a representative MetRS1 from Staphylococcus aureus (SaMetRS) in its apo and substrate-binding forms. The connecting peptide (CP) domain of SaMetRS differs from HcMetRS in structural organization and dynamic movement. We screened 1049 chemical fragments against SaMetRS preincubated with or without substrate ATP, and ten hits were identified. Four cocrystal structures revealed that the fragments bound to either the L-Met binding site or an auxiliary pocket near the tRNA CCA end binding site of SaMetRS. Interestingly, fragment binding was enhanced by ATP in most cases, suggesting a potential ATP-assisted ligand binding mechanism in MetRS1. Moreover, co-binding with ATP was also observed in our cocrystal structure of SaMetRS with a class of newly reported inhibitors that simultaneously occupied the auxiliary pocket, tRNA site and L-Met site. Our findings will inspire the development of new MetRS1 inhibitors for fighting microbial infections.

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Organizational Affiliation: 

Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine--tRNA ligase	A	530	Staphylococcus aureus	Mutation(s): 0  Gene Names: metG EC: 6.1.1.10
UniProt
Find proteins for Q5HII6 (Staphylococcus aureus (strain COL)) Explore Q5HII6  Go to UniProtKB:  Q5HII6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1V7 (Subject of Investigation/LOI)	B [auth A]	2-(4-bromanyl-3-oxidanyl-phenyl)-1-[(1R)-2-[2-(2-tert-butylphenoxy)ethanoylamino]-1-(3,4-dimethoxyphenyl)ethyl]-N-methyl-benzimidazole-5-carboxamide C37 H39 Br N4 O6 NVXVCMOQLYUYSD-LJAQVGFWSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.237 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.492	α = 90
b = 80.331	β = 90
c = 117.961	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
autoPROC	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2022-01-24 
• Released Date: 2022-04-27 
Deposition Author(s): Yi, J., Cai, Z., Qiu, H., Lu, F., Chen, B., Luo, Z., Gu, Q., Xu, J., Zhou, H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22177140
National Natural Science Foundation of China (NSFC)	China	81773636

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2022-05-18
  Changes: Database references