PDBsum entry 1qrt

Ligase/RNA

PDB id

1qrt

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Contents

			Protein chain

					529 a.a. *

			DNA/RNA

			Ligands

					ATP

			Waters ×72

* Residue conservation analysis

PDB id:

1qrt

Links

Name:

Ligase/RNA

Title:

Glutaminyl-tRNA synthetase mutant d235g complexed with glutamine transfer RNA

Structure:

Trnagln2. Chain: b. Synonym: glutamine transfer RNA. Engineered: yes. Protein (glutaminyl-tRNA synthetase . Chain: a. Synonym: glutaminyl-tRNA ligase. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: k-12. Variant: deltah1deltatrp. Gene: trnagln2. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: lambda pl promoter. Strain: x3r2 (glns deletion strain).

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å

R-factor:

0.216

Authors:

J.G.Arnez,T.A.Steitz

Key ref:

J.G.Arnez and T.A.Steitz (1996). Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP. Biochemistry, 35, 14725-14733. PubMed id: 8942633 DOI: 10.1021/bi961532o

Date:

14-Jun-96

Release date:

07-Dec-96

PROCHECK

	Headers

	References

Protein chain

P00962 (SYQ_ECOLI) - Glutamine--tRNA ligase from Escherichia coli (strain K12)

Seq: Struc:

Seq: Struc:					554 a.a. 529 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chain

G-G-G-G-U-A-U-C-G-C-C-A-A-G-C-G-G-U-A-A-G-G-C-A-C-C-G-G-A-U-U-C-U-G-A-U-U-C-C- 74 bases



		Enzyme reactions

Enzyme class:

E.C.6.1.1.18 - glutamine--tRNA ligase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

tRNA(Gln) + L-glutamine + ATP = L-glutaminyl-tRNA(Gln) + AMP + diphosphate

tRNA(Gln)
Bound ligand (Het Group name = ATP)
corresponds exactly

L-glutamine

ATP

L-glutaminyl-tRNA(Gln)

AMP

diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi961532o	Biochemistry 35:14725-14733 (1996)
PubMed id: 8942633

Crystal structures of three misacylating mutants of Escherichia coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP.
J.G.Arnez, T.A.Steitz.

ABSTRACT

Three previously described mutant Escherichia coli glutaminyl-tRNA synthetase (GlnRS) proteins that incorrectly aminoacylate the amber suppressor derived from tRNATyr (supF) with glutamine were cocrystallized with wild-type tRNAGln and their structures determined. In two of the mutant enzymes studied, Asp235, which contacts base pair G3-C70 in the acceptor stem, has been changed to asparagine in GlnRS7 and to glycine in GlnRS10. These mutations result in changed interactions between Asn235 of GlnRS7 and G3-C70 of the tRNA and an altered water structure between Gly235 of GlnRS10 and base pair G3-C70. These structures suggest how the mutant enzymes can show only small changes in their ability to aminoacylate wild-type cognate tRNA on the one hand and yet show a lack of discrimination against a noncognate U3-A70 base pair on the other. In contrast, the change of Ile129 to Thr in GlnRS15 causes virtually no change in the structure of the complex, and the explanation for its ability to misacylate supF is unclear.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20139416

M.G.Gagnon, Y.I.Boutorine, and S.V.Steinberg (2010).
Recurrent RNA motifs as probes for studying RNA-protein interactions in the ribosome.

Nucleic Acids Res, 38, 3441-3453.

18160411

N.J.Reiter, L.J.Maher, and S.E.Butcher (2008).
DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.

Nucleic Acids Res, 36, 1227-1236.

PDB code:

2jwv

17366653

G.He, A.Patra, K.Siegmund, M.Peter, K.Heeg, A.Dalpke, and C.Richert (2007).
Immunostimulatory CpG Oligonucleotides Form Defined Three-Dimensional Structures: Results from an NMR Study.

ChemMedChem, 2, 549-560.

17447878

I.A.Vasil'eva, and N.A.Moor (2007).
Interaction of aminoacyl-tRNA synthetases with tRNA: general principles and distinguishing characteristics of the high-molecular-weight substrate recognition.

Biochemistry (Mosc), 72, 247-263.

14523926

P.Pfister, S.Hobbie, Q.Vicens, E.C.Böttger, and E.Westhof (2003).
The molecular basis for A-site mutations conferring aminoglycoside resistance: relationship between ribosomal susceptibility and X-ray crystal structures.

Chembiochem, 4, 1078-1088.

12177293

N.B.Leontis, J.Stombaugh, and E.Westhof (2002).
The non-Watson-Crick base pairs and their associated isostericity matrices.

Nucleic Acids Res, 30, 3497-3531.

10713991

K.A.Denessiouk, and M.S.Johnson (2000).
When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.

Proteins, 38, 310-326.

10966471

M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.

Annu Rev Biochem, 69, 617-650.

9657697

J.Liu, M.Ibba, K.W.Hong, and D.Söll (1998).
The terminal adenosine of tRNA(Gln) mediates tRNA-dependent amino acid recognition by glutaminyl-tRNA synthetase.

Biochemistry, 37, 9836-9842.

9729611

M.K.Berlyn (1998).
Linkage map of Escherichia coli K-12, edition 10: the traditional map.

Microbiol Mol Biol Rev, 62, 814-984.

9562563

V.L.Rath, L.F.Silvian, B.Beijer, B.S.Sproat, and T.A.Steitz (1998).
How glutaminyl-tRNA synthetase selects glutamine.

Structure, 6, 439-449.

PDB code:

1qtq

9372178

J.L.Riechmann, and E.M.Meyerowitz (1997).
MADS domain proteins in plant development.

Biol Chem, 378, 1079-1101.

9396794

M.Sissler, G.Eriani, F.Martin, R.Giegé, and C.Florentz (1997).
Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase.

Nucleic Acids Res, 25, 4899-4906.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.