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PDBsum entry 1eov

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Ligase PDB id
1eov
Jmol PyMol
Contents
Protein chain
487 a.a. *
Waters ×227
* Residue conservation analysis
PDB id:
1eov
Name: Ligase
Title: Free aspartyl-tRNA synthetase (asprs) (E.C. 6.1.1.12) from y
Structure: Aspartyl-tRNA synthetase. Chain: a. Fragment: engineered asprs monomer lacking the 70 n-termina acid residues. Synonym: asprs. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: aps gene. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.202     R-free:   0.242
Authors: C.Sauter,B.Lorber,J.Cavarelli,D.Moras,R.Giege
Key ref:
C.Sauter et al. (2000). The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain. J Mol Biol, 299, 1313-1324. PubMed id: 10873455 DOI: 10.1006/jmbi.2000.3791
Date:
24-Mar-00     Release date:   24-Sep-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P04802  (SYDC_YEAST) -  Aspartate--tRNA ligase, cytoplasmic
Seq:
Struc:
 
Seq:
Struc:
557 a.a.
487 a.a.
Key:    PfamA domain  PfamB 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     tRNA aminoacylation for protein translation   2 terms 
  Biochemical function     nucleotide binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.2000.3791 J Mol Biol 299:1313-1324 (2000)
PubMed id: 10873455  
 
 
The free yeast aspartyl-tRNA synthetase differs from the tRNA(Asp)-complexed enzyme by structural changes in the catalytic site, hinge region, and anticodon-binding domain.
C.Sauter, B.Lorber, J.Cavarelli, D.Moras, R.Giegé.
 
  ABSTRACT  
 
Aminoacyl-tRNA synthetases catalyze the specific charging of amino acid residues on tRNAs. Accurate recognition of a tRNA by its synthetase is achieved through sequence and structural signalling. It has been shown that tRNAs undergo large conformational changes upon binding to enzymes, but little is known about the conformational rearrangements in tRNA-bound synthetases. To address this issue the crystal structure of the dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast was solved in its free form and compared to that of the protein associated to the cognate tRNA(Asp). The use of an enzyme truncated in N terminus improved the crystal quality and allowed us to solve and refine the structure of free AspRS at 2.3 A resolution. For the first time, snapshots are available for the different macromolecular states belonging to the same tRNA aminoacylation system, comprising the free forms for tRNA and enzyme, and their complex. Overall, the synthetase is less affected by the association than the tRNA, although significant local changes occur. They concern a rotation of the anticodon binding domain and a movement in the hinge region which connects the anticodon binding and active-site domains in the AspRS subunit. The most dramatic differences are observed in two evolutionary conserved loops. Both are in the neighborhood of the catalytic site and are of importance for ligand binding. The combination of this structural analysis with mutagenesis and enzymology data points to a tRNA binding process that starts by a recognition event between the tRNA anticodon loop and the synthetase anticodon binding module.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Stereoview of the electron density in the class II b-sheet region of the apo-enzyme active-site domain (from the left to the right, strands A2 to A6). The s[a] weighted 2mF[obs] -DF[calc] density was contoured at 1.3s. The right panel gives a schematic representation of these five central b-strands with their orientation and sequence. Gray circles indicate amino acid residues with C^a atoms pointing toward the reader.
Figure 4.
Figure 4. Comparison of free and tRNA bound AspRS subunits. The picture shows the free monomer (gray) superimposed to subunit B (green) in the complex with tRNA (blue). Monomers A and B in the structure of AspRS-ATP-tRNA^Asp ternary complex are related by a non-crystallographic 2-fold axis (Cavarelli et al., 1994). The two stereo views are turned by 90° with respect to each other. Monomers were superimposed by least squares minimization of the active-site seven stranded b-sheet (49 C^a).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 1313-1324) copyright 2000.  
  Figures were selected by an automated process.  

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
21119764 R.Giegé, and C.Sauter (2010).
Biocrystallography: past, present, future.
  HFSP J, 4, 109-121.  
19386587 F.Charrière, P.O'Donoghue, S.Helgadóttir, L.Maréchal-Drouard, M.Cristodero, E.K.Horn, D.Söll, and A.Schneider (2009).
Dual Targeting of a tRNAAsp Requires Two Different Aspartyl-tRNA Synthetases in Trypanosoma brucei.
  J Biol Chem, 284, 16210-16217.  
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.  
18611382 L.Klipcan, I.Levin, N.Kessler, N.Moor, I.Finarov, and M.Safro (2008).
The tRNA-induced conformational activation of human mitochondrial phenylalanyl-tRNA synthetase.
  Structure, 16, 1095-1104.
PDB code: 3cmq
17898174 A.Ghosh, and S.Vishveshwara (2007).
A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis.
  Proc Natl Acad Sci U S A, 104, 15711-15716.  
17172343 C.Wang, B.W.Sobral, and K.P.Williams (2007).
Loss of a universal tRNA feature.
  J Bacteriol, 189, 1954-1962.  
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.  
17444518 R.Sathyapriya, and S.Vishveshwara (2007).
Structure networks of E. coli glutaminyl-tRNA synthetase: effects of ligand binding.
  Proteins, 68, 541-550.  
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.  
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.  
12684518 M.Goto, R.Omi, I.Miyahara, M.Sugahara, and K.Hirotsu (2003).
Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction.
  J Biol Chem, 278, 22964-22971.
PDB codes: 1j1z 1j20 1j21 1kh3
12486031 M.Ryckelynck, R.Giegé, and M.Frugier (2003).
Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase.
  J Biol Chem, 278, 9683-9690.  
11125115 M.Szymanski, M.A.Deniziak, and J.Barciszewski (2001).
Aminoacyl-tRNA synthetases database.
  Nucleic Acids Res, 29, 288-290.  
11054826 A.Blasco, and P.Sanz (2000).
Current awareness on yeast.
  Yeast, 16, 1449-1456.  
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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