PDBsum entry 1iq0

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protein links
Ligase PDB id
Protein chain
588 a.a. *
Waters ×196
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Thermus thermophilus arginyl-tRNA synthetase
Structure: Arginyl-tRNA synthetase. Chain: a. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: args. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.30Å     R-factor:   0.215     R-free:   0.242
Authors: A.Shimada,O.Nureki,M.Goto,S.Takahashi,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
A.Shimada et al. (2001). Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase. Proc Natl Acad Sci U S A, 98, 13537-13542. PubMed id: 11698642 DOI: 10.1073/pnas.231267998
24-May-01     Release date:   28-Nov-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q93RP5  (Q93RP5_THETH) -  Arginine--tRNA ligase
592 a.a.
588 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Arginine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg)
+ L-arginine
+ tRNA(Arg)
+ diphosphate
+ L-arginyl-tRNA(Arg)
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     5 terms  


DOI no: 10.1073/pnas.231267998 Proc Natl Acad Sci U S A 98:13537-13542 (2001)
PubMed id: 11698642  
Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
A.Shimada, O.Nureki, M.Goto, S.Takahashi, S.Yokoyama.
Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNA(Arg): A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNA(Arg). In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from Thermus thermophilus at 2.3 A resolution. The structure of the T. thermophilus ArgRS was found to be similar to that of the previously reported S. cerevisiae ArgRS, except for short insertions and a concomitant conformational change in the N-terminal domain. The structure of the yeast ArgRS.tRNA(Arg) complex suggested that two residues in the unique N-terminal domain, Tyr(77) and Asn(79), which are phylogenetically invariant in the ArgRSs from all organisms with A20 in tRNA(Arg)s, are involved in A20 recognition. However, in a docking model constructed based on the yeast ArgRS.tRNA(Arg) and T. thermophilus ArgRS structures, Tyr(77) and Asn(79) are not close enough to make direct contact with A20, because of the conformational change in the N-terminal domain. Nevertheless, the replacement of Tyr(77) or Asn(79) by Ala severely reduced the arginylation efficiency. Therefore, some conformational change around A20 is necessary for the recognition. Surprisingly, the N79D mutant equally recognized A20 and G20, with only a slight reduction in the arginylation efficiency as compared with the wild-type enzyme. Other mutants of Asn(79) also exhibited broader specificity for the nucleotide at position 20 of tRNA(Arg). We propose a model of A20 recognition by the ArgRS that is consistent with the present results of the mutational analyses.
  Selected figure(s)  
Figure 3.
Fig. 3. (A) The structure of the S. cerevisiae ArgRS complexed with tRNA^Arg. The tRNA is indicated as a yellow tube. The side chains of Asn106, Phe^109, and Gln111, and D20 and C34 are depicted as a ball and stick representation. (B) A docking model of the T. thermophilus ArgRS and tRNA. The side chains of Tyr77 and Asn79, and G34, C35, the discriminator G73, and the predicted A20 are depicted as a ball and stick representation.
Figure 4.
Fig. 4. (A) Interaction of the S. cerevisiae ArgRS with D20. Hydrogen bonds between D20 and Asn106, and that between D20 and Gln111, are indicated as dashed lines. (B) The docking model of the T. thermophilus ArgRS and tRNA. A20 and the side chains of Val74, Tyr77, and Asn79 are depicted as a ball and stick representation. (C) A model of A20 recognition by Tyr77 and Asn79, based on the present mutagenesis analyses. Putative hydrogen bonds formed between the modeled A20 and Asn79, and that between Asn79 and Pro33, are indicated as dashed lines. (D, E, F, and G) Schematic representations of possible interactions between A20 and Asn79 (D), G20 and Asn79 (E), G20 and Asp79 (F), and A20 and Asp79 (G). Possible hydrogen bonds are indicated as dashed lines.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19952117 S.Shaul, D.Berel, Y.Benjamini, and D.Graur (2010).
Revisiting the operational RNA code for amino acids: Ensemble attributes and their implications.
  RNA, 16, 141-153.  
  19193994 A.Eichert, A.Schreiber, J.P.Fürste, M.Perbandt, C.Betzel, V.A.Erdmann, and C.Förster (2009).
Escherichia coli tRNA(Arg) acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 98.  
19656186 M.Konno, T.Sumida, E.Uchikawa, Y.Mori, T.Yanagisawa, S.Sekine, and S.Yokoyama (2009).
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
  FEBS J, 276, 4763-4779.
PDB codes: 2zue 2zuf
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.  
17061034 M.Zhou, A.Azzi, X.Xia, E.D.Wang, and S.X.Lin (2007).
Crystallization and preliminary X-ray diffraction analysis of E. coli arginyl-tRNA synthetase in complex form with a tRNAArg.
  Amino Acids, 32, 479-482.  
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.  
15317795 K.Sakamoto, S.Ishimaru, T.Kobayashi, J.R.Walker, and S.Yokoyama (2004).
The Escherichia coli argU10(Ts) phenotype is caused by a reduction in the cellular level of the argU tRNA for the rare codons AGA and AGG.
  J Bacteriol, 186, 5899-5905.  
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
15208367 Y.G.Zheng, H.Wei, C.Ling, F.Martin, G.Eriani, and E.D.Wang (2004).
Two distinct domains of the beta subunit of Aquifex aeolicus leucyl-tRNA synthetase are involved in tRNA binding as revealed by a three-hybrid selection.
  Nucleic Acids Res, 32, 3294-3303.  
12737813 J.Cavarelli (2003).
Pushing induced fit to its limits: tRNA-dependent active site assembly in class I aminoacyl-tRNA synthetases.
  Structure, 11, 484-486.  
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.  
14690419 R.Geslain, G.Bey, J.Cavarelli, and G.Eriani (2003).
Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding.
  Biochemistry, 42, 15092-15101.  
12554668 S.Sekine, O.Nureki, D.Y.Dubois, S.Bernier, R.Chênevert, J.Lapointe, D.G.Vassylyev, and S.Yokoyama (2003).
ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding.
  EMBO J, 22, 676-688.
PDB codes: 1j09 1n75 1n77 1n78
11717415 T.L.Hendrickson (2001).
Recognizing the D-loop of transfer RNAs.
  Proc Natl Acad Sci U S A, 98, 13473-13475.  
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.