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PDBsum entry 1eqr

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protein metals Protein-protein interface(s) links
Ligase PDB id
1eqr
Jmol
Contents
Protein chains
590 a.a. *
Metals
_MG ×3
Waters ×427
* Residue conservation analysis
PDB id:
1eqr
Name: Ligase
Title: Crystal structure of free aspartyl-tRNA synthetase from escherichia coli
Structure: Aspartyl-tRNA synthetase. Chain: a, b, c. Synonym: asprs. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.70Å     R-factor:   0.198     R-free:   0.269
Authors: B.Rees,G.Webster,M.Delarue,M.Boeglin,D.Moras
Key ref:
B.Rees et al. (2000). Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates. J Mol Biol, 299, 1157-1164. PubMed id: 10873442 DOI: 10.1006/jmbi.2000.3792
Date:
06-Apr-00     Release date:   29-Jun-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P21889  (SYD_ECOLI) -  Aspartate--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
590 a.a.
590 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   2 terms 
  Biological process     translation   3 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3792 J Mol Biol 299:1157-1164 (2000)
PubMed id: 10873442  
 
 
Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates.
B.Rees, G.Webster, M.Delarue, M.Boeglin, D.Moras.
 
  ABSTRACT  
 
The crystal structure of aspartyl-tRNA synthetase from Escherichia coli has been determined to a resolution of 2.7 A. The structure is compared to the same enzyme co-crystallized with tRNA(Asp) and containing aspartyl adenylate or ATP. The asymmetric unit contains three monomers of the enzyme. While most parts of the protein show no significant differences in the three monomers, a few regions cannot be superimposed. Those regions are characterized by a high B-factor, and consist mostly of loops that make contacts with the tRNA in the complexes. The flexibility of the protein is seen at a global level, by the observation of a 10 to 15 degrees rotation of the N-terminal and insertion domains upon tRNA binding, and at the level of the individual amino acid residues, by main-chain and side-chain rearrangements. In contrast to these induced-fit conformational changes, a few residues essential for the tRNA anticodon or aspartyl-adenylate recognition exist in a predefined conformation, ensured by specific interactions within the protein.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Superposition of the free AspRS on the E. coli AspRS-tRNA complex (Eiler et al., 1999), in stereoview. The C^a backbones of the three monomers (mol1, mol2 and mol3) of the crystal asymmetric unit are shown in red, the C^a and phosphate backbones of the complex in blue. The superposition is made on the core of the active-site domain (see the text). The axes of the additional rotation necessary for the best superposition of the other domains (highlighted in brighter colors) are shown as broken lines. These Figures were made using MOLSCRIPT (Kraulis, 1991). In all three monomers, upon binding to the tRNA, the additional rotations bring the N-terminal domain (at the bottom of each figure) closer to the tRNA anticodon loop, and the insertion domain (top left) closer to the acceptor arm.
Figure 3.
Figure 3. Detailed comparisons between free AspRS (pink), and the AspRS-tRNA^Asp-aspartyl adenylate complex (blue, with the ligands in gray): (a) The anticodon recognizing region; (b) two arginine residues making direct or indirect contacts with the begining of the anticodon stem; (c) and (d) two different views of the residues in contact with the adenylate. These Figures were made with MOLSCRIPT (Kraulis, 1991) and RASTER 3D (Merrit & Murphy, 1994). Notice the conformational stability of a few key residues responsible for the recognition of the anticodon (Arg76, Glu93, Gln46) and of the aspartyl moiety of the adenylate ligand (Arg489, Glu235, Lys198, Asp233), in sharp contrast with the conformational changes of most of the residues coming in contact with the ligands.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 1157-1164) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19734148 J.Jaric, S.Bilokapic, S.Lesjak, A.Crnkovic, N.Ban, and I.Weygand-Durasevic (2009).
Identification of amino acids in the N-terminal domain of atypical methanogenic-type Seryl-tRNA synthetase critical for tRNA recognition.
  J Biol Chem, 284, 30643-30651.  
19228694 S.Bilokapic, N.Ivic, V.Godinic-Mikulcic, I.Piantanida, N.Ban, and I.Weygand-Durasevic (2009).
Idiosyncratic Helix-Turn-Helix Motif in Methanosarcina barkeri Seryl-tRNA Synthetase Has a Critical Architectural Role.
  J Biol Chem, 284, 10706-10713.  
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.  
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.  
17964262 M.Bailly, M.Blaise, B.Lorber, H.D.Becker, and D.Kern (2007).
The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis.
  Mol Cell, 28, 228-239.  
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.  
15665334 T.Spreter, M.Pech, and B.Beatrix (2005).
The crystal structure of archaeal nascent polypeptide-associated complex (NAC) reveals a unique fold and the presence of a ubiquitin-associated domain.
  J Biol Chem, 280, 15849-15854.
PDB code: 1tr8
15840835 Y.Zhang, L.Wang, P.G.Schultz, and I.A.Wilson (2005).
Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine.
  Protein Sci, 14, 1340-1349.
PDB codes: 1u7d 1u7x
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
14625589 J.J.Song, J.Liu, N.H.Tolia, J.Schneiderman, S.K.Smith, R.A.Martienssen, G.J.Hannon, and L.Joshua-Tor (2003).
The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes.
  Nat Struct Biol, 10, 1026-1032.
PDB code: 1r6z
14581222 S.Mohan, N.Sinha, and S.J.Smith-Gill (2003).
Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity.
  Biophys J, 85, 3221-3236.  
11371463 D.Jain, K.J.Kaur, and D.M.Salunke (2001).
Plasticity in protein-peptide recognition: crystal structures of two different peptides bound to concanavalin A.
  Biophys J, 80, 2912-2921.
PDB codes: 1jui 1jyc
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.