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PDBsum entry 1qrt

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protein dna_rna ligands links
Ligase/RNA PDB id
1qrt
Jmol
Contents
Protein chain
529 a.a. *
DNA/RNA
Ligands
ATP
Waters ×72
* Residue conservation analysis
PDB id:
1qrt
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.
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
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00962  (SYQ_ECOLI) -  Glutamine--tRNA ligase
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)

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.18  - Glutamine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-glutamine + tRNA(Gln) = AMP + diphosphate + L-glutaminyl- tRNA(Gln)
ATP
Bound ligand (Het Group name = ATP)
corresponds exactly
+ L-glutamine
+ tRNA(Gln)
= AMP
+ diphosphate
+ L-glutaminyl- tRNA(Gln)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     translation   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    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.