1QU3

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

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

  • 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 ...

    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.

    Related Citations: 
    • Metal Ions that Stabilize the tRNA and Mediate the Recognition by its Cognate Synthetase
      Wang, J., Silvian, L.F., Steitz, T.A.
      () To be published --: --
    • Switching from a Resting to Synthetic and Hydrolytic Modes in Editing tRNA Synthetases
      Wang, J., Silvian, L.F., Steitz, T.A.
      () To be published --: --
    • Structure Based Drug Design Against Mupirocin Resistant Staphylococcus Aureus
      Wang, J., Silvian, L.F., Steitz, T.A.
      () To be published --: --
    Organizational Affiliation: 

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



Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ISOLEUCYL-TRNA SYNTHETASE A917Staphylococcus aureusMutation(s): 0 
Gene Names: ileS
EC: 6.1.1.5
Find proteins for P41972 (Staphylococcus aureus)
Explore P41972 
Go to UniProtKB:  P41972
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
ISOLEUCYL-TRNAT75Staphylococcus aureus
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MRC
Query on MRC
Download Ideal Coordinates CCD File 
A
MUPIROCIN
C26 H44 O9
MINDHVHHQZYEEK-DWJPPWIMSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.345 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71α = 90
b = 100β = 90
c = 180γ = 90

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

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