1QU2 | pdb_00001qu2

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.281 (Depositor), 0.290 (DCC)
R-Value Work:
0.239 (Depositor), 0.245 (DCC)
R-Value Observed:
0.239 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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

PubMed: 10446055 Search on PubMed
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P41972
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
ISOLEUCYL-TRNA	A [auth T]	75	Staphylococcus aureus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRC Query on MRC Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	MUPIROCIN C₂₆ H₄₄ O₉ MINDHVHHQZYEEK-HBBNESRFSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A]	N [auth A], O [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain C [auth T] MOL2 format, chain C [auth T] mmCIF format, chain C [auth T]	C [auth T]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth T] Interactions & Density Focus chain C [auth T]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth T] SDF format, chain E [auth T] SDF format, chain F [auth T] SDF format, chain G [auth T] SDF format, chain H [auth T] SDF format, chain I [auth T] SDF format, chain J [auth T] SDF format, chain K [auth T] SDF format, chain L [auth T] SDF format, chain M [auth T] MOL2 format, chain D [auth T] MOL2 format, chain E [auth T] MOL2 format, chain F [auth T] MOL2 format, chain G [auth T] MOL2 format, chain H [auth T] MOL2 format, chain I [auth T] MOL2 format, chain J [auth T] MOL2 format, chain K [auth T] MOL2 format, chain L [auth T] MOL2 format, chain M [auth T] mmCIF format, chain D [auth T] mmCIF format, chain E [auth T] mmCIF format, chain F [auth T] mmCIF format, chain G [auth T] mmCIF format, chain H [auth T] mmCIF format, chain I [auth T] mmCIF format, chain J [auth T] mmCIF format, chain K [auth T] mmCIF format, chain L [auth T] mmCIF format, chain M [auth T]	D [auth T] E [auth T] F [auth T] G [auth T] H [auth T] 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		Interactions Focus chain D [auth T] Focus chain E [auth T] Focus chain F [auth T] Focus chain G [auth T] Focus chain H [auth T] Focus chain I [auth T] Focus chain J [auth T] Focus chain K [auth T] Focus chain L [auth T] Focus chain M [auth T] Interactions & Density Focus chain D [auth T] Focus chain E [auth T] Focus chain F [auth T] Focus chain G [auth T] Focus chain H [auth T] Focus chain I [auth T] Focus chain J [auth T] Focus chain K [auth T] Focus chain L [auth T] Focus chain M [auth T]

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 (Depositor), 0.290 (DCC)
R-Value Work: 0.239 (Depositor), 0.245 (DCC)
R-Value Observed: 0.239 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1999-08-31

Deposition Author(s):

Silvian, L.F.

Wang, J.

Steitz, T.A.

Revision History (Full details and data files)

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