8C8U | pdb_00008c8u

Priestia megaterium mupirocin-resistant isoleucyl-tRNA synthetase 2 complexed with mupirocin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.222 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif.

Brkic, A.Leibundgut, M.Jablonska, J.Zanki, V.Car, Z.Petrovic Perokovic, V.Marsavelski, A.Ban, N.Gruic-Sovulj, I.

(2023) Nat Commun 14: 5498-5498

  • DOI: https://doi.org/10.1038/s41467-023-41244-3
  • Primary Citation Related Structures: 
    8C8U, 8C8V, 8C8W, 8C9D, 8C9E, 8C9F, 8C9G

  • PubMed Abstract: 

    Antibiotics target key biological processes that include protein synthesis. Bacteria respond by developing resistance, which increases rapidly due to antibiotics overuse. Mupirocin, a clinically used natural antibiotic, inhibits isoleucyl-tRNA synthetase (IleRS), an enzyme that links isoleucine to its tRNA Ile for protein synthesis. Two IleRSs, mupirocin-sensitive IleRS1 and resistant IleRS2, coexist in bacteria. The latter may also be found in resistant Staphylococcus aureus clinical isolates. Here, we describe the structural basis of mupirocin resistance and unravel a mechanism of hyper-resistance evolved by some IleRS2 proteins. We surprisingly find that an up to 10 3 -fold increase in resistance originates from alteration of the HIGH motif, a signature motif of the class I aminoacyl-tRNA synthetases to which IleRSs belong. The structural analysis demonstrates how an altered HIGH motif could be adopted in IleRS2 but not IleRS1, providing insight into an elegant mechanism for coevolution of the key catalytic motif and associated antibiotic resistance.


  • Organizational Affiliation
    • Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia.

Macromolecule Content 

  • Total Structure Weight: 119.09 kDa 
  • Atom Count: 9,055 
  • Modeled Residue Count: 1,028 
  • Deposited Residue Count: 1,032 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoleucine--tRNA ligase1,032Priestia megateriumMutation(s): 0 
Gene Names: ileSBG04_5198
EC: 6.1.1.5
UniProt
Find proteins for A0A0B6AVD3 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19))
Explore A0A0B6AVD3 
Go to UniProtKB:  A0A0B6AVD3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B6AVD3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MRC
(Subject of Investigation/LOI)

Query on MRC



Download:Ideal Coordinates CCD File
C [auth A]MUPIROCIN
C26 H44 O9
MINDHVHHQZYEEK-HBBNESRFSA-N
1PE

Query on 1PE



Download:Ideal Coordinates CCD File
G [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
TLA

Query on TLA



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A],
D [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.222 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.58α = 90
b = 124.83β = 90
c = 114.46γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Croatian Science FoundationCroatia180567
Swiss National Science FoundationSwitzerland180567
European Regional Development FundEuropean UnionKK.01.1.1.02.0016

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-23
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Database references