1QU2

INSIGHTS INTO EDITING FROM AN ILE-TRNA SYNTHETASE STRUCTURE WITH TRNA(ILE) AND MUPIROCIN

• PDB DOI: https://doi.org/10.2210/pdb1QU2/pdb
• NAKB: 1QU2

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


• Deposited: 1999-07-06 Released: 1999-08-31 
• Deposition Author(s): Silvian, L.F., Wang, J., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.281 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 

Literature

Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.

Silvian, L.F., Wang, J., Steitz, T.A.

(1999) Science 285: 1074-1077

• PubMed: 10446055 
• Primary Citation of Related Structures:  
  1FFY, 1QU2, 1QU3


• PubMed Abstract: 
  

  Isoleucyl-transfer RNA (tRNA) synthetase (IleRS) joins Ile to tRNA(Ile) at its synthetic active site and hydrolyzes incorrectly acylated amino acids at its editing active site. The 2.2 angstrom resolution crystal structure of Staphylococcus aureus IleRS complexed with tRNA(Ile) and Mupirocin shows the acceptor strand of the tRNA(Ile) in the continuously stacked, A-form conformation with the 3' terminal nucleotide in the editing active site. To position the 3' terminus in the synthetic active site, the acceptor strand must adopt the hairpinned conformation seen in tRNA(Gln) complexed with its synthetase. The amino acid editing activity of the IleRS may result from the incorrect products shuttling between the synthetic and editing active sites, which is reminiscent of the editing mechanism of DNA polymerases.

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Organizational Affiliation: 

Department of Molecular Biophysics, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520-8114, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 130.21 kDa 
• Atom Count: 9,386 
• Modelled Residue Count: 992 
• Deposited Residue Count: 992 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOLEUCYL-TRNA SYNTHETASE	B [auth A]	917	Staphylococcus aureus	Mutation(s): 0  EC: 6.1.1.5
UniProt
Find proteins for P41972 (Staphylococcus aureus) Explore P41972  Go to UniProtKB:  P41972

Entity ID: 1
Molecule	Chains	Length	Organism	Image
ISOLEUCYL-TRNA	A [auth T]	75	Staphylococcus aureus

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MRC	P [auth A]	MUPIROCIN C26 H44 O9 MINDHVHHQZYEEK-HBBNESRFSA-N
ZN	N [auth A], O [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	C [auth T]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	D [auth T], E [auth T], F [auth T], G [auth T], H [auth T], I [auth T], J [auth T], K [auth T], L [auth T], M [auth T]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MRC	BindingDB:  1QU2	IC50: min: 0.85, max: 279 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.281 
• R-Value Work: 0.239 
• R-Value Observed: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71	α = 90
b = 100	β = 90
c = 186	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-08-31 
Deposition Author(s): Silvian, L.F., Wang, J., Steitz, T.A.

Revision History  

• Version 1.0: 1999-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Structure summary