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PDBsum entry 1efw

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protein dna_rna Protein-protein interface(s) links
Ligase/RNA PDB id
1efw
Jmol
Contents
Protein chains
580 a.a. *
DNA/RNA
Waters ×96
* Residue conservation analysis
PDB id:
1efw
Name: Ligase/RNA
Title: Crystal structure of aspartyl-tRNA synthetase from thermus thermophilus complexed to trnaasp from escherichia coli
Structure: Aspartyl-tRNA. Chain: c, d. Engineered: yes. Aspartyl-tRNA synthetase. Chain: a, b. Synonym: aspartate - tRNA ligase, asprs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Thermus thermophilus. Organism_taxid: 274. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
3.00Å     R-factor:   0.248     R-free:   0.293
Authors: C.Briand,A.Poterszman,S.Eiler,G.Webster,J.-C.Thierry,D.Moras
Key ref:
C.Briand et al. (2000). An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase. J Mol Biol, 299, 1051-1060. PubMed id: 10843857 DOI: 10.1006/jmbi.2000.3819
Date:
10-Feb-00     Release date:   19-Jun-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P36419  (SYD_THETH) -  Aspartate--tRNA(Asp) ligase
Seq:
Struc:
 
Seq:
Struc:
580 a.a.
580 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.12  - Aspartate--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp)
ATP
+ L-aspartate
+ tRNA(Asp)
= AMP
+ diphosphate
+ L-aspartyl-tRNA(Asp)
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   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3819 J Mol Biol 299:1051-1060 (2000)
PubMed id: 10843857  
 
 
An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase.
C.Briand, A.Poterszman, S.Eiler, G.Webster, J.Thierry, D.Moras.
 
  ABSTRACT  
 
The crystal structures of aspartyl-tRNA synthetase (AspRS) from Thermus thermophilus, a prokaryotic class IIb enzyme, complexed with tRNA(Asp) from either T. thermophilus or Escherichia coli reveal a potential intermediate of the recognition process. The tRNA is positioned on the enzyme such that it cannot be aminoacylated but adopts an overall conformation similar to that observed in active complexes. While the anticodon loop binds to the N-terminal domain of the enzyme in a manner similar to that of the related active complexes, its aminoacyl acceptor arm remains at the entrance of the active site, stabilized in its intermediate conformational state by non-specific interactions with the insertion and catalytic domains. The thermophilic nature of the enzyme, which manifests itself in a very low kinetic efficiency at 17 degrees C, the temperature at which the crystals were grown, is in agreement with the relative stability of this non-productive conformational state. Based on these data, a pathway for tRNA binding and recognition is proposed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The T. thermophilus AspRS system. (a) Cloverleaf representation of tt-tRNA^Asp [Keith et al 1993]. The identity nucleotides are shown in red [Becker et al 1997a]. (b) Arrhenius plot of ATP-PPi exchange catalysed by ttAspRS. (c) A ribbon representation of the ttAspRS:ec-tRNA^Asp complex viewed down the molecular dimer axis. Each monomer contains an N-terminal domain (residues 1 to 106, in yellow), a hinge domain (residues 107 to 136, in green) an active site domain (residues 137 to 277 and 416 to 580, in blue and magenta) and an insertion domain (residues 278 to 415, in orange). Each tRNA (grey) interacts with the four domains of one monomer. The Figure was made using SETOR [Evans 1993].
Figure 3.
Figure 3. Footprint of the tRNA on AspRS. AspRS surface buried by the tRNA in the (a) E. coli system [Eiler et al 1999] and (b)T. thermophilus (this work). Protein surface patches located at less than 3.5 Å from the tRNA (see Material and Methods) are drawn in magenta. The interaction surfaces are similar for the N-terminal domain, but vary considerably through the rest of the complexes. In the ttAspRS:tRNA^Asp complex, few interactions are observed with the hinge domain and almost none with the active site. (c) Superposition of the phosphate backbones of ec-tRNA^Asp in complex with ttAspRS (orange) and ec-tRNA^Asp in active complex with ecAspRS (green). The phosphate backbones superimpose with an rmsd of 1.74 Å over 73 phosphate atoms. (d) Representation of the phosphate backbone of ec-tRNA^Asp complexed to ttAspRS (orange) and ecAspRS (green) after superposition of both AspRSs on their anticodon binding domain (rmsd of 0.37 Å over 52 C^a atoms). (e) Ribbon representation of the ttAspRS:ec-tRNA^Asp complex in orange and ecAspRS:ec-tRNA^Asp complex in green after superposition of both enzymes on the b-sheet of the catalytic domain (rmsd of 0.47 Å over 51 C^a atoms). The tRNA remains partially outside of the catalytic site of the enzyme in the ttAspRS: ec-tRNA^Asp complex. The distance between the phosphorus atoms of C72 is 7.0 Å. (a) and (b) were made using GRASP [Nicholls et al 1991], (c), (d) and (e) were made using SETOR [Evans 1993].
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 1051-1060) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19118381 K.Nozawa, P.O'Donoghue, S.Gundllapalli, Y.Araiso, R.Ishitani, T.Umehara, D.Söll, and O.Nureki (2009).
Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality.
  Nature, 457, 1163-1167.
PDB codes: 2zni 2znj
18076053 D.Thompson, C.Lazennec, P.Plateau, and T.Simonson (2008).
Probing electrostatic interactions and ligand binding in aspartyl-tRNA synthetase through site-directed mutagenesis and computer simulations.
  Proteins, 71, 1450-1460.  
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
17172343 C.Wang, B.W.Sobral, and K.P.Williams (2007).
Loss of a universal tRNA feature.
  J Bacteriol, 189, 1954-1962.  
17690095 D.Thompson, C.Lazennec, P.Plateau, and T.Simonson (2007).
Ammonium scanning in an enzyme active site. The chiral specificity of aspartyl-tRNA synthetase.
  J Biol Chem, 282, 30856-30868.  
17317626 E.C.Guth, and C.S.Francklyn (2007).
Kinetic discrimination of tRNA identity by the conserved motif 2 loop of a class II aminoacyl-tRNA synthetase.
  Mol Cell, 25, 531-542.  
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.  
  17620724 K.Suzuki, Y.Sato, Y.Maeda, S.Shimizu, M.T.Hossain, S.Ubukata, T.Sekiguchi, and A.Takénaka (2007).
Crystallization and preliminary X-ray crystallographic study of a putative aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 608-612.  
16741232 A.E.Rosen, B.S.Brooks, E.Guth, C.S.Francklyn, and K.Musier-Forsyth (2006).
Evolutionary conservation of a functionally important backbone phosphate group critical for aminoacylation of histidine tRNAs.
  RNA, 12, 1315-1322.  
16774919 D.Thompson, and T.Simonson (2006).
Molecular dynamics simulations show that bound Mg2+ contributes to amino acid and aminoacyl adenylate binding specificity in aspartyl-tRNA synthetase through long range electrostatic interactions.
  J Biol Chem, 281, 23792-23803.  
16800632 P.Chuawong, and T.L.Hendrickson (2006).
The nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori: anticodon-binding domain mutations that impact tRNA specificity and heterologous toxicity.
  Biochemistry, 45, 8079-8087.  
16724112 X.L.Yang, F.J.Otero, K.L.Ewalt, J.Liu, M.A.Swairjo, C.Köhrer, U.L.RajBhandary, R.J.Skene, D.E.McRee, and P.Schimmel (2006).
Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis.
  EMBO J, 25, 2919-2929.
PDB code: 2azx
15289581 F.Martin, S.Barends, and G.Eriani (2004).
Single amino acid changes in AspRS reveal alternative routes for expanding its tRNA repertoire in vivo.
  Nucleic Acids Res, 32, 4081-4089.  
15121895 P.S.Klosterman, D.K.Hendrix, M.Tamura, S.R.Holbrook, and S.E.Brenner (2004).
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns.
  Nucleic Acids Res, 32, 2342-2352.  
12766171 A.Brevet, J.Chen, S.Commans, C.Lazennec, S.Blanquet, and P.Plateau (2003).
Anticodon recognition in evolution: switching tRNA specificity of an aminoacyl-tRNA synthetase by site-directed peptide transplantation.
  J Biol Chem, 278, 30927-30935.  
12660169 C.Charron, H.Roy, M.Blaise, R.Giegé, and D.Kern (2003).
Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain.
  EMBO J, 22, 1632-1643.
PDB code: 1n9w
12730374 L.Feng, D.Tumbula-Hansen, H.Toogood, and D.Soll (2003).
Expanding tRNA recognition of a tRNA synthetase by a single amino acid change.
  Proc Natl Acad Sci U S A, 100, 5676-5681.  
11953757 A.Torres-Larios, A.C.Dock-Bregeon, P.Romby, B.Rees, R.Sankaranarayanan, J.Caillet, M.Springer, C.Ehresmann, B.Ehresmann, and D.Moras (2002).
Structural basis of translational control by Escherichia coli threonyl tRNA synthetase.
  Nat Struct Biol, 9, 343-347.
PDB code: 1kog
11914489 J.D.Ng, C.Sauter, B.Lorber, N.Kirkland, J.Arnez, and R.Giegé (2002).
Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination.
  Acta Crystallogr D Biol Crystallogr, 58, 645-652.
PDB code: 1l0w
11566892 L.Moulinier, S.Eiler, G.Eriani, J.Gangloff, J.C.Thierry, K.Gabriel, W.H.McClain, and D.Moras (2001).
The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.
  EMBO J, 20, 5290-5301.
PDB code: 1il2
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 codes are shown on the right.