7D5C | pdb_00007d5c

IleRS in complex with a tRNA site inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7D5C/pdb

• Classification: LIGASE/INHIBITOR
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-09-25 Released: 2021-02-24 
• Deposition Author(s): Chen, B., Luo, S., Zhou, H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase.

Chen, B., Luo, S., Zhang, S., Ju, Y., Gu, Q., Xu, J., Yang, X.L., Zhou, H.

(2021) Nat Commun 12: 1616-1616

• PubMed: 33712620 
• DOI: https://doi.org/10.1038/s41467-021-21902-0
• Primary Citation Related Structures: 
  7D5C


• PubMed Abstract: 
  

  The polyketide natural product reveromycin A (RM-A) exhibits antifungal, anticancer, anti-bone metastasis, anti-periodontitis and anti-osteoporosis activities by selectively inhibiting eukaryotic cytoplasmic isoleucyl-tRNA synthetase (IleRS). Herein, a co-crystal structure suggests that the RM-A molecule occupies the substrate tRNA ^Ile binding site of Saccharomyces cerevisiae IleRS (ScIleRS), by partially mimicking the binding of tRNA ^Ile . RM-A binding is facilitated by the copurified intermediate product isoleucyl-adenylate (Ile-AMP). The binding assays confirm that RM-A competes with tRNA ^Ile while binding synergistically with L-isoleucine or intermediate analogue Ile-AMS to the aminoacylation pocket of ScIleRS. This study highlights that the vast tRNA binding site of the Rossmann-fold catalytic domain of class I aminoacyl-tRNA synthetases could be targeted by a small molecule. This finding will inform future rational drug design.

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Organizational Affiliation: 
• Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, 92037, USA.
Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. [e-mail].
Research Center for Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 115.41 kDa 
• Atom Count: 8,273 
• Modeled Residue Count: 919 
• Deposited Residue Count: 992 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoleucine--tRNA ligase, cytoplasmic	A	992	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: ILS1, YBL076C, YBL0734 EC: 6.1.1.5
UniProt
Find proteins for P09436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09436  Go to UniProtKB:  P09436

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GVU (Subject of Investigation/LOI)	B [auth A]	(2E,4S,5S,6E,8E)-10-[(2S,3R,6S,8R,9S)-3-butyl-9-methyl-2-[(1E,3E)-3-methyl-5-oxidanyl-5-oxidanylidene-penta-1,3-dienyl]-3-(4-oxidanyl-4-oxidanylidene-butanoyl)oxy-1,7-dioxaspiro[5.5]undecan-8-yl]-4,8-dimethyl-5-oxidanyl-deca-2,6,8-trienoic acid C36 H52 O11 ZESGNAJSBDILTB-OXVOKJAASA-N
GV6 (Subject of Investigation/LOI)	C [auth A]	[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S,3S)-2-azanyl-3-methyl-pentanoate C16 H25 N6 O8 P ACZWYNUJBRLCEC-XATJSACLSA-N
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.649	α = 90
b = 64.758	β = 107.78
c = 142.229	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-24 
Deposition Author(s): Chen, B., Luo, S., Zhou, H.

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

Revision History  

• Version 1.0: 2021-02-24
  Type: Initial release
  
• Version 1.1: 2021-03-24
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description