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PDBsum entry 1euy

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protein dna_rna ligands links
Ligase/RNA PDB id
1euy
Jmol
Contents
Protein chain
529 a.a. *
DNA/RNA
Ligands
QSI
Waters ×54
* Residue conservation analysis
PDB id:
1euy
Name: Ligase/RNA
Title: Glutaminyl-tRNA synthetase complexed with a tRNA mutant and an active site inhibitor
Structure: Glutaminyl tRNA. Chain: b. Engineered: yes. Glutaminyl-tRNA synthetase. Chain: a. Synonym: glnrs, glutamine-tRNA ligase. Engineered: yes
Source: Synthetic: yes. Other_details: product of runoff t7 polymerase transcription from synthetic DNA template. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.234     R-free:   0.277
Authors: L.D.Sherlin,T.L.Bullock,K.J.Newberry,R.S.A.Lipman,Y.-M.Hou, B.Beijer,B.S.Sproat,J.J.Perona
Key ref:
L.D.Sherlin et al. (2000). Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases. J Mol Biol, 299, 431-446. PubMed id: 10860750 DOI: 10.1006/jmbi.2000.3749
Date:
19-Apr-00     Release date:   04-Jun-00    
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

 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
+ L-glutamine
+ tRNA(Gln)
=
AMP
Bound ligand (Het Group name = QSI)
matches with 52.00% similarity
+ 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: 10.1006/jmbi.2000.3749 J Mol Biol 299:431-446 (2000)
PubMed id: 10860750  
 
 
Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases.
L.D.Sherlin, T.L.Bullock, K.J.Newberry, R.S.Lipman, Y.M.Hou, B.Beijer, B.S.Sproat, J.J.Perona.
 
  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.
 
  Selected figure(s)  
 
Figure 6.
Figure 6. Hydrogen bonding interactions of the 15-48 Levitt pair in tRNA^Gln (top; [Rould et al 1991]), tRNA^Cys (center; [Nissen et al 1999]) and the Gln04 mutant (bottom). The distances (in Å) between the electronegative atoms of the hydrogen-bonding pair are indicated.
Figure 8.
Figure 8. (a) Superposition of the structures of wild-type tRNA^Gln (bound to GlnRS and QSI) with the Gln04 mutant, in the region of the 15-48 Levitt pair. The superposition is based on backbone atoms of the protein (residues 8-547). The wild-type structure is shown in blue and green and the Gln04 mutant in red and yellow. (b) Divergent stereo view of the superposition in (a) with the same color-coding. Nucleotide U8 of both structures and nucleotides U46 and U47 of wild-type are removed for clarity. The new tertiary hydrogen bond formed in the Gln04 mutant is indicated by the broken black line.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 431-446) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
17449728 L.E.Sanderson, and O.C.Uhlenbeck (2007).
The 51-63 base pair of tRNA confers specificity for binding by EF-Tu.
  RNA, 13, 835-840.  
15845536 I.Gruic-Sovulj, N.Uter, T.Bullock, and J.J.Perona (2005).
tRNA-dependent aminoacyl-adenylate hydrolysis by a nonediting class I aminoacyl-tRNA synthetase.
  J Biol Chem, 280, 23978-23986.
PDB code: 1zjw
15489861 S.Hauenstein, C.M.Zhang, Y.M.Hou, and J.J.Perona (2004).
Shape-selective RNA recognition by cysteinyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 1134-1141.
PDB code: 1u0b
12810913 C.Evilia, X.Ming, S.Dassarma, and Y.M.Hou (2003).
Aminoacylation of an unusual tRNA(Cys) from an extreme halophile.
  RNA, 9, 794-801.  
  11720294 L.D.Sherlin, T.L.Bullock, T.A.Nissan, J.J.Perona, F.J.Lariviere, O.C.Uhlenbeck, and S.A.Scaringe (2001).
Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization.
  RNA, 7, 1671-1678.  
11125115 M.Szymanski, M.A.Deniziak, and J.Barciszewski (2001).
Aminoacyl-tRNA synthetases database.
  Nucleic Acids Res, 29, 288-290.  
11105758 T.A.Nissan, and J.J.Perona (2000).
Alternative designs for construction of the class II transfer RNA tertiary core.
  RNA, 6, 1585-1596.  
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.