1EUQ

CRYSTAL STRUCTURE OF GLUTAMINYL-TRNA SYNTHETASE COMPLEXED WITH A TRNA-GLN MUTANT AND AN ACTIVE-SITE INHIBITOR

PDB DOI: 10.2210/pdb1EUQ/pdb
NDB: PR0025

Classification: ligase/RNA
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-04-17 Released: 2000-06-04
Deposition Author(s): Sherlin, L.D., Bullock, T.L., Newberry, K.J., Lipman, R.S.A., Hou, Y.-M., Beijer, B., Sproat, B.S., Perona, J.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.285
R-Value Work: 0.242

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases.

Sherlin, L.D., Bullock, T.L., Newberry, K.J., Lipman, R.S., Hou, Y.M., Beijer, B., Sproat, B.S., Perona, J.J.

(2000) J Mol Biol 299: 431-446

PubMed: 10860750 Search on PubMed
DOI: 10.1006/jmbi.2000.3749
Primary Citation of Related Structures:
1EUQ, 1EUY

PubMed Abstract:

The position of the tertiary Levitt pair between nucleotides 15 and 48 in the transfer RNA core region suggests a key role in stabilizing the joining of the two helical domains, and in maintaining the relative orientations of the D and variable loops. E. coli tRNA(Gln) possesses the canonical Pu15-Py48 trans pairing at this position (G15-C48), while the tRNA(Cys) species from this organism instead features an unusual G15-G48 pair. To explore the structural context dependence of a G15-G48 Levitt pair, a number of tRNA(Gln) species containing G15-G48 were constructed and evaluated as substrates for glutaminyl and cysteinyl-tRNA synthetases. The glutaminylation efficiencies of these mutant tRNAs are reduced by two to tenfold compared with native tRNA(Gln), consistent with previous findings that the tertiary core of this tRNA plays a role in GlnRS recognition. Introduction of tRNA(Cys) identity nucleotides at the acceptor and anticodon ends of tRNA(Gln) produced a tRNA substrate which was efficiently aminoacylated by CysRS, even though the tertiary core region of this species contains the tRNA(Gln) G15-C48 pair. Surprisingly, introduction of G15-G48 into the non-cognate tRNA(Gln) tertiary core then significantly impairs CysRS recognition. By contrast, previous work has shown that CysRS aminoacylates tRNA(Cys) core regions containing G15-G48 with much better efficiency than those with G15-C48. Therefore, tertiary nucleotides surrounding the Levitt pair must significantly modulate the efficiency of aminoacylation by CysRS. To explore the detailed nature of the structural interdependence, crystal structures of two tRNA(Gln) mutants containing G15-G48 were determined bound to GlnRS. These structures show that the larger purine ring of G48 is accommodated by rotation into the syn position, with the N7 nitrogen serving as hydrogen bond acceptor from several groups of G15. The G15-G48 conformations differ significantly compared to that observed in the native tRNA(Cys) structure bound to EF-Tu, further implicating an important role for surrounding nucleotides in maintaining the integrity of the tertiary core and its consequent ability to present crucial recognition determinants to aminoacyl-tRNA synthetases.

Organizational Affiliation:

Department of Chemistry and Biochemistry, and Interdepartmental Program in Biochemistry and Molecular Biology, University of California at Santa Barbara, Santa Barbara, CA, 93106-9510, USA.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMINYL-TRNA SYNTHETASE	B [auth A]	548	Escherichia coli	Mutation(s): 0 EC: 6.1.1.18
UniProt
Find proteins for P00962 (Escherichia coli (strain K12)) Explore P00962 Go to UniProtKB: P00962
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00962
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
GLUTAMINYL TRNA	A [auth B]	72	N/A
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QSI Query on QSI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	5'-O-[N-(L-GLUTAMINYL)-SULFAMOYL]ADENOSINE C₁₅ H₂₂ N₈ O₈ S KXWKSWRGZLZHEF-WERHYGNASA-N		Ligand Interaction