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PDBsum entry 1il2
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protein dna_rna ligands Protein-protein interface(s) links
Ligase/RNA PDB id
1il2

 

 

 

 

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Contents
Protein chains
585 a.a. *
DNA/RNA
Ligands
SO4 ×2
AMO ×2
Waters ×402
* Residue conservation analysis
PDB id:
1il2
Name: Ligase/RNA
Title: Crystal structure of the e. Coli aspartyl-tRNA synthetase:yeast trnaasp:aspartyl-adenylate complex
Structure: Aspartyl transfer RNA. Chain: c, d. Aspartyl-tRNA synthetase. Chain: a, b. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
2.60Å     R-factor:   0.204     R-free:   0.257
Authors: L.Moulinier,S.Eiler,G.Eriani,J.Gangloff,J.C.Thierry,K.Gabriel, W.H.Mcclain,D.Moras
Key ref:
L.Moulinier et al. (2001). The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism. EMBO J, 20, 5290-5301. PubMed id: 11566892 DOI: 10.1093/emboj/20.18.5290
Date:
07-May-01     Release date:   28-Sep-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P21889  (SYD_ECOLI) -  Aspartate--tRNA ligase from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		590 a.a.
585 a.a.
Key:    Secondary structure  CATH domain

DNA/RNA chains
  U-C-C-G-U-G-A-U-A-G-U-U-PSU-A-A-H2U-G-G-H2U-C-A-G-A-A-U-G-G-G-C-G-C-PSU-U-G-U- 75 bases
  C-C-G-U-G-A-U-A-G-U-U-PSU-A-A-H2U-G-G-H2U-C-A-G-A-A-U-G-G-G-C-G-C-PSU-U-G-U-C- 70 bases

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.12  - aspartate--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: tRNA(Asp) + L-aspartate + ATP = L-aspartyl-tRNA(Asp) + AMP + diphosphate
tRNA(Asp)
 + L-aspartate
 + ATP
 =
L-aspartyl-tRNA(Asp)
Bound ligand (Het Group name = AMO)
matches with 74.19% similarity 		+ AMP
 + diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1093/emboj/20.18.5290 EMBO J 20:5290-5301 (2001)
PubMed id: 11566892  
 
 
The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism.
L.Moulinier, S.Eiler, G.Eriani, J.Gangloff, J.C.Thierry, K.Gabriel, W.H.McClain, D.Moras.
 
  ABSTRACT  
 
The 2.6 A resolution crystal structure of an inactive complex between yeast tRNA(Asp) and Escherichia coli aspartyl-tRNA synthetase reveals the molecular details of a tRNA-induced mechanism that controls the specificity of the reaction. The dimer is asymmetric, with only one of the two bound tRNAs entering the active site cleft of its subunit. However, the flipping loop, which controls the proper positioning of the amino acid substrate, acts as a lid and prevents the correct positioning of the terminal adenosine. The structure suggests that the acceptor stem regulates the loop movement through sugar phosphate backbone- protein interactions. Solution and cellular studies on mutant tRNAs confirm the crucial role of the tRNA three-dimensional structure versus a specific recognition of bases in the control mechanism.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 (A) General view of the dimeric aspartyl-tRNA synthetase from E.coli complexed with yeast tRNA^Asp and aspartyl-adenylate. The tRNA^Asp molecules, colored in red and yellow, are bound to one protein subunit shown in brown and white, respectively. (B) AspRS surface buried by the tRNA in monomer 1 (left) and monomer 2 (right) calculated and displayed using GRASP (Nicholls and Honig, 1991). The surface is colored according to a distance array between the two molecular surfaces: distances <2.5 Å between the tRNA and the enzyme are drawn in green, and distances between 2.5 and 3.5 Å are in yellow. The interaction surfaces are highly similar for the protein N-terminal domain in both monomers but vary through the rest of the complex. (C) Ribbon representation of one AspRS subunit in gray (monomer 1) of the heterologous complex with the bound yeast tRNA^Asp in yellow. The E.coli tRNA^Asp as seen in the cognate complex is drawn in blue after superposition of the enzymes on their active sites. (D) Relative position of the two tRNAs of the heterologous complex. Superposition was optimized on the two subunit active sites. The tRNA^Asp from monomer 1 is drawn in yellow, the tRNA from monomer 2 in red. (E) Comparison of the tRNA molecule from monomer 2 of the heterologous complex (red) and the free (uncomplexed) yeast tRNA^Asp (green) (Moras et al., 1980). Figures 3, Figures 4, 5 were generated using the Program SETOR (Evans, 1998). 		Figure 4.
Figure 4 Yeast tRNA^Asp acceptor stem in monomer 1 (A) and monomer 2 (B) showing the U -G mismatches. The tRNA acceptor stem in monomer 1 is bound to the enzymes and shows a regular RNA conformation for the backbone dihedral angles and (gauche-/gauche+); the distance between the phosphorus atoms of G68 and C69 is 5.6 Å. The tRNA molecule in monomer 2 shows no contact between the acceptor stem and the protein. As a consequence, the dihedral angles and are trans/trans for G68, and the distance between the phosphorus atoms of G68 and C69 is 6.6 Å. 'Accommodation' of U -G mismatches has already been observed for the yeast AspRS -tRNA^Asp complex (equivalent to tRNA 1) and for the free tRNA (equivalent to tRNA 2). (C) Recognition of the discriminator base G73 of yeast tRNA^Asp by the E.coli AspRS. The hydrogen bonds between the protein and the nucleic acid are shown as yellow dotted lines. They are similar to those observed in the homologous E.coli AspRS -tRNA^Asp complex.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 5290-5301) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19874856 E.A.Merritt, T.L.Arakaki, E.T.Larson, A.Kelley, N.Mueller, A.J.Napuli, L.Zhang, G.Deditta, J.Luft, C.L.Verlinde, E.Fan, F.Zucker, F.S.Buckner, W.C.Van Voorhis, and W.G.Hol (2010).
Crystal structure of the aspartyl-tRNA synthetase from Entamoeba histolytica.
  Mol Biochem Parasitol, 169, 95.
PDB code: 3i7f
20670890 W.W.Navarre, S.B.Zou, H.Roy, J.L.Xie, A.Savchenko, A.Singer, E.Edvokimova, L.R.Prost, R.Kumar, M.Ibba, and F.C.Fang (2010).
PoxA, yjeK, and elongation factor P coordinately modulate virulence and drug resistance in Salmonella enterica.
  Mol Cell, 39, 209-221.
PDB code: 3g1z
19443655 T.Bour, A.Akaddar, B.Lorber, S.Blais, C.Balg, E.Candolfi, and M.Frugier (2009).
Plasmodial Aspartyl-tRNA Synthetases and Peculiarities in Plasmodium falciparum.
  J Biol Chem, 284, 18893-18903.  
18997014 A.Minajigi, and C.S.Francklyn (2008).
RNA-assisted catalysis in a protein enzyme: The 2'-hydroxyl of tRNA(Thr) A76 promotes aminoacylation by threonyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 105, 17748-17753.  
18850722 C.S.Francklyn (2008).
DNA polymerases and aminoacyl-tRNA synthetases: shared mechanisms for ensuring the fidelity of gene expression.
  Biochemistry, 47, 11695-11703.  
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.  
18548004 H.Xiao, H.Murakami, H.Suga, and A.R.Ferré-D'Amaré (2008).
Structural basis of specific tRNA aminoacylation by a small in vitro selected ribozyme.
  Nature, 454, 358-361.
PDB codes: 3cul 3cun
18836497 R.Giegé (2008).
Toward a more complete view of tRNA biology.
  Nat Struct Mol Biol, 15, 1007-1014.  
18310681 S.An, G.Barany, and K.Musier-Forsyth (2008).
Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase.
  Nucleic Acids Res, 36, 2514-2521.  
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.  
17301225 S.Kamtekar, M.J.Hohn, H.S.Park, M.Schnitzbauer, A.Sauerwald, D.Söll, and T.A.Steitz (2007).
Toward understanding phosphoseryl-tRNACys formation: the crystal structure of Methanococcus maripaludis phosphoseryl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 104, 2620-2625.
PDB code: 2odr
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.  
16597625 A.Fender, C.Sauter, M.Messmer, J.Pütz, R.Giegé, C.Florentz, and M.Sissler (2006).
Loss of a primordial identity element for a mammalian mitochondrial aminoacylation system.
  J Biol Chem, 281, 15980-15986.  
16574659 A.Metlitskaya, T.Kazakov, A.Kommer, O.Pavlova, M.Praetorius-Ibba, M.Ibba, I.Krasheninnikov, V.Kolb, I.Khmel, and K.Severinov (2006).
Aspartyl-tRNA synthetase is the target of peptide nucleotide antibiotic Microcin C.
  J Biol Chem, 281, 18033-18042.  
16408313 D.Thompson, P.Plateau, and T.Simonson (2006).
Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetase.
  Chembiochem, 7, 337-344.  
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.  
16317719 S.J.Hughes, J.A.Tanner, A.D.Miller, and I.R.Gould (2006).
Molecular dynamics simulations of LysRS: an asymmetric state.
  Proteins, 62, 649-662.  
16537400 W.H.McClain (2006).
Surprising contribution to aminoacylation and translation of non-Watson-Crick pairs in tRNA.
  Proc Natl Acad Sci U S A, 103, 4570-4575.  
14681579 D.Lee, and W.H.McClain (2004).
Aptamer redesigned tRNA is nonfunctional and degraded in cells.
  RNA, 10, 7.  
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.  
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
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.  
12581659 A.R.Ferré-D'Amaré (2003).
RNA-modifying enzymes.
  Curr Opin Struct Biol, 13, 49-55.  
12775689 B.Min, M.Kitabatake, C.Polycarpo, J.Pelaschier, G.Raczniak, B.Ruan, H.Kobayashi, S.Namgoong, and D.Söll (2003).
Protein synthesis in Escherichia coli with mischarged tRNA.
  J Bacteriol, 185, 3524-3526.  
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
12649491 H.Choi, K.Gabriel, J.Schneider, S.Otten, and W.H.McClain (2003).
Recognition of acceptor-stem structure of tRNA(Asp) by Escherichia coli aspartyl-tRNA synthetase.
  RNA, 9, 386-393.  
12874385 H.Roy, H.D.Becker, J.Reinbolt, and D.Kern (2003).
When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism.
  Proc Natl Acad Sci U S A, 100, 9837-9842.  
12907713 R.Geslain, F.Martin, A.Camasses, and G.Eriani (2003).
A yeast knockout strain to discriminate between active and inactive tRNA molecules.
  Nucleic Acids Res, 31, 4729-4737.  
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
12458790 C.Francklyn, J.J.Perona, J.Puetz, and Y.M.Hou (2002).
Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation.
  RNA, 8, 1363-1372.  
11847123 F.Walter, J.Pütz, R.Giegé, and E.Westhof (2002).
Binding of tobramycin leads to conformational changes in yeast tRNA(Asp) and inhibition of aminoacylation.
  EMBO J, 21, 760-768.  
12392560 I.Gruic-Sovulj, I.Landeka, D.Söll, and I.Weygand-Durasevic (2002).
tRNA-dependent amino acid discrimination by yeast seryl-tRNA synthetase.
  Eur J Biochem, 269, 5271-5279.  
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.

 

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