PDBsum entry 1qu2

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protein dna_rna ligands metals links
Ligase/RNA PDB id
Protein chain
917 a.a. *
_MG ×10
_ZN ×2
Waters ×328
* Residue conservation analysis
PDB id:
Name: Ligase/RNA
Title: Insights into editing from an ile-tRNA synthetase structure with tRNA(ile) and mupirocin
Structure: Isoleucyl-tRNA. Chain: t. Engineered: yes. Isoleucyl-tRNA synthetase. Chain: a. Synonym: isoleucine--tRNA ligase, ilers. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
2.20Å     R-factor:   0.239     R-free:   0.281
Authors: L.F.Silvian,J.Wang,T.A.Steitz
Key ref:
L.F.Silvian et al. (1999). Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. Science, 285, 1074-1077. PubMed id: 10446055 DOI: 10.1126/science.285.5430.1074
06-Jul-99     Release date:   31-Aug-99    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P41972  (SYI1_STAAU) -  Isoleucine--tRNA ligase
917 a.a.
917 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Isoleucine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-isoleucine + tRNA(Ile) = AMP + diphosphate + L-isoleucyl- tRNA(Ile)
+ L-isoleucine
+ tRNA(Ile)
+ diphosphate
+ L-isoleucyl- tRNA(Ile)
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   4 terms 
  Biochemical function     aminoacyl-tRNA editing activity     9 terms  


DOI no: 10.1126/science.285.5430.1074 Science 285:1074-1077 (1999)
PubMed id: 10446055  
Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin.
L.F.Silvian, J.Wang, T.A.Steitz.
Isoleucyl-transfer RNA (tRNA) synthetase (IleRS) joins Ile to tRNA(Ile) at its synthetic active site and hydrolyzes incorrectly acylated amino acids at its editing active site. The 2.2 angstrom resolution crystal structure of Staphylococcus aureus IleRS complexed with tRNA(Ile) and Mupirocin shows the acceptor strand of the tRNA(Ile) in the continuously stacked, A-form conformation with the 3' terminal nucleotide in the editing active site. To position the 3' terminus in the synthetic active site, the acceptor strand must adopt the hairpinned conformation seen in tRNA(Gln) complexed with its synthetase. The amino acid editing activity of the IleRS may result from the incorrect products shuttling between the synthetic and editing active sites, which is reminiscent of the editing mechanism of DNA polymerases.
  Selected figure(s)  
Figure 1.
Fig. 1. (A) Structure of the isoleucyl-tRNA synthetase complex with tRNA^Ile and Mupirocin. The ordered portion of the tRNA is shown in gold and the two modeled nucleotides are in silver. The Mupirocin drug is in pink. The protein is colored by domain or by section: NH[2]-terminal region (orange), Rossmann fold (green), editing domain or CP1 (yellow), acceptor stem binding domain (gray), CP2 domain (blue), helical domain (pink), COOH-terminal junction (turquoise), and Zn-binding domain (red). (B) Experimental electron density for the 3' end of the tRNA^Ile. Good density specifies the positions of Ade^73 (A73) and Cyt^74 (C74), but little density exists for the Cyt^75 (C75) and Ade^76 (A76) nucleotides, which are model-built to extend the A-form conformation.
Figure 2.
Fig. 2. (A) Superposition of the acceptor stems of complexed tRNA^Ile (gray thick line), complexed tRNA^Gln (black thin line), and uncomplexed tRNA^Phe (light thick line). The acceptor strand of tRNA^Ile is similar to the continuously stacked conformation of tRNA^Phe but differs from the hairpinned conformation of tRNA^Gln. (B) and (C) Superposition of tRNA^Gln on tRNA^Ile on a solvent contact surface representation of IleRS. The acceptor strand of tRNA^Ile, represented as a ribbon, is observed at the editing active site. Homology modeling of the tRNA^Gln hairpin conformation (ball and stick representation) places its 3' terminus in the synthetic active site 34 Å away. Two orientations are shown to display the active site pockets and the cleft running between them.
  The above figures are reprinted by permission from the AAAs: Science (1999, 285, 1074-1077) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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PDB codes: 4aq7 4arc 4ari 4as1
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PDB code: 3prh
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Structural basis of tRNA agmatinylation essential for AUA codon decoding.
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PDB codes: 3amt 3amu 3au7
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PDB code: 3ip4
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19285947 J.Ling, B.R.So, S.S.Yadavalli, H.Roy, S.Shoji, K.Fredrick, K.Musier-Forsyth, and M.Ibba (2009).
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19379069 J.Ling, N.Reynolds, and M.Ibba (2009).
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The C-Ala domain brings together editing and aminoacylation functions on one tRNA.
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PDB code: 3g98
19423669 M.Naganuma, S.Sekine, R.Fukunaga, and S.Yokoyama (2009).
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
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PDB codes: 2ztg 2zvf
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19053270 L.W.Tremblay, F.Fan, M.W.Vetting, and J.S.Blanchard (2008).
The 1.6 A crystal structure of Mycobacterium smegmatis MshC: the penultimate enzyme in the mycothiol biosynthetic pathway.
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PDB code: 3c8z
19020078 M.T.Boniecki, M.T.Vu, A.K.Betha, and S.A.Martinis (2008).
CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase.
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DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.
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PDB code: 2jwv
18367476 P.Yao, B.Zhu, S.Jaeger, G.Eriani, and E.D.Wang (2008).
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The CP2 domain of leucyl-tRNA synthetase is crucial for amino acid activation and post-transfer editing.
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17474713 A.K.Betha, A.M.Williams, and S.A.Martinis (2007).
Isolated CP1 domain of Escherichia coli leucyl-tRNA synthetase is dependent on flanking hinge motifs for amino acid editing activity.
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17447878 I.A.Vasil'eva, and N.A.Moor (2007).
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17894371 J.E.Stone, J.C.Phillips, P.L.Freddolino, D.J.Hardy, L.G.Trabuco, and K.Schulten (2007).
Accelerating molecular modeling applications with graphics processors.
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Mechanism of tRNA-dependent editing in translational quality control.
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17804641 J.Ling, S.S.Yadavalli, and M.Ibba (2007).
Phenylalanyl-tRNA synthetase editing defects result in efficient mistranslation of phenylalanine codons as tyrosine.
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Predicting helical coaxial stacking in RNA multibranch loops.
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A single residue in leucyl-tRNA synthetase affecting amino acid specificity and tRNA aminoacylation.
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17925437 W.Li, and J.Frank (2007).
Transfer RNA in the hybrid P/E state: correlating molecular dynamics simulations with cryo-EM data.
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Multiple mechanisms to ameliorate the fitness burden of mupirocin resistance in Salmonella typhimurium.
  Mol Microbiol, 64, 1038-1048.  
16505383 A.M.Williams, and S.A.Martinis (2006).
Mutational unmasking of a tRNA-dependent pathway for preventing genetic code ambiguity.
  Proc Natl Acad Sci U S A, 103, 3586-3591.  
17043414 J.A.Yang, D.W.Park, J.W.Sohn, I.S.Yang, K.H.Kim, and M.J.Kim (2006).
Molecular analysis of isoleucyl-tRNA synthetase mutations in clinical isolates of methicillin-resistant Staphylococcus aureus with low-level mupirocin resistance.
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16397872 M.L.Mock, T.Michon, J.C.van Hest, and D.A.Tirrell (2006).
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17027500 T.Crepin, A.Yaremchuk, M.Tukalo, and S.Cusack (2006).
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.
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PDB codes: 2i4l 2i4m 2i4n 2i4o 2j3l 2j3m
16902403 T.Hussain, S.P.Kruparani, B.Pal, A.C.Dock-Bregeon, S.Dwivedi, M.R.Shekar, K.Sureshbabu, and R.Sankaranarayanan (2006).
Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea.
  EMBO J, 25, 4152-4162.
PDB codes: 2hkz 2hl0 2hl1 2hl2
15856481 J.Roach, S.Sharma, M.Kapustina, and C.W.Carter (2005).
Structure alignment via Delaunay tetrahedralization.
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15894617 K.Nakanishi, S.Fukai, Y.Ikeuchi, A.Soma, Y.Sekine, T.Suzuki, and O.Nureki (2005).
Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine-specific loop and a tRNA-recognition domain.
  Proc Natl Acad Sci U S A, 102, 7487-7492.
PDB code: 1wy5
16155581 K.Nakanishi, Y.Ogiso, T.Nakama, S.Fukai, and O.Nureki (2005).
Structural basis for anticodon recognition by methionyl-tRNA synthetase.
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PDB codes: 2csx 2ct8
16155583 M.Tukalo, A.Yaremchuk, R.Fukunaga, S.Yokoyama, and S.Cusack (2005).
The crystal structure of leucyl-tRNA synthetase complexed with tRNALeu in the post-transfer-editing conformation.
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PDB codes: 2bte 2byt
15775966 M.W.Zhao, B.Zhu, R.Hao, M.G.Xu, G.Eriani, and E.D.Wang (2005).
Leucyl-tRNA synthetase from the ancestral bacterium Aquifex aeolicus contains relics of synthetase evolution.
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Crystallization of leucyl-tRNA synthetase complexed with tRNALeu from the archaeon Pyrococcus horikoshii.
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16155584 R.Fukunaga, and S.Yokoyama (2005).
Aminoacylation complex structures of leucyl-tRNA synthetase and tRNALeu reveal two modes of discriminator-base recognition.
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Expansion of the genetic code in yeast: making life more complex.
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15240874 D.Korencic, I.Ahel, J.Schelert, M.Sacher, B.Ruan, C.Stathopoulos, P.Blum, M.Ibba, and D.Söll (2004).
A freestanding proofreading domain is required for protein synthesis quality control in Archaea.
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15526031 H.Roy, J.Ling, M.Irnov, and M.Ibba (2004).
Post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-tRNA synthetase.
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A domain for editing by an archaebacterial tRNA synthetase.
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PDB code: 1u0b
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  Proc Natl Acad Sci U S A, 100, 490-494.  
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Transiently misacylated tRNA is a primer for editing of misactivated adenylates by class I aminoacyl-tRNA synthetases.
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Identification of functional similarities between proteins using directed evolution.
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The long-range electrostatic interactions control tRNA-aminoacyl-tRNA synthetase complex formation.
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Tools for the automatic identification and classification of RNA base pairs.
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Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability.
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tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase.
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PDB code: 1nyl
14690420 M.L.Bovee, M.A.Pierce, and C.S.Francklyn (2003).
Induced fit and kinetic mechanism of adenylation catalyzed by Escherichia coli threonyl-tRNA synthetase.
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Limited set of amino acid residues in a class Ia aminoacyl-tRNA synthetase is crucial for tRNA binding.
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Isoleucyl-tRNA synthetase mutations in Staphylococcus aureus clinical isolates and in vitro selection of low-level mupirocin-resistant strains.
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12554880 S.Fukai, O.Nureki, S.Sekine, A.Shimada, D.G.Vassylyev, and S.Yokoyama (2003).
Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase.
  RNA, 9, 100-111.
PDB codes: 1ivs 1iyw
12578991 S.Kamtekar, W.D.Kennedy, J.Wang, C.Stathopoulos, D.Söll, and T.A.Steitz (2003).
The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases.
  Proc Natl Acad Sci U S A, 100, 1673-1678.
PDB codes: 1nj1 1nj2 1nj5 1nj6 1nj8
12771213 X.Du, and E.D.Wang (2003).
Tertiary structure base pairs between D- and TpsiC-loops of Escherichia coli tRNA(Leu) play important roles in both aminoacylation and editing.
  Nucleic Acids Res, 31, 2865-2872.  
11782529 A.C.Bishop, T.K.Nomanbhoy, and P.Schimmel (2002).
Blocking site-to-site translocation of a misactivated amino acid by mutation of a class I tRNA synthetase.
  Proc Natl Acad Sci U S A, 99, 585-590.  
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.  
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.  
12034843 K.D.Tardif, and J.Horowitz (2002).
Transfer RNA determinants for translational editing by Escherichia coli valyl-tRNA synthetase.
  Nucleic Acids Res, 30, 2538-2545.  
12032090 K.J.Newberry, Y.M.Hou, and J.J.Perona (2002).
Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase.
  EMBO J, 21, 2778-2787.
PDB codes: 1li5 1li7
11796355 M.Antonio, N.McFerran, and M.J.Pallen (2002).
Mutations affecting the Rossman fold of isoleucyl-tRNA synthetase are correlated with low-level mupirocin resistance in Staphylococcus aureus.
  Antimicrob Agents Chemother, 46, 438-442.  
12486008 S.B.Rho, T.L.Lincecum, and S.A.Martinis (2002).
An inserted region of leucyl-tRNA synthetase plays a critical role in group I intron splicing.
  EMBO J, 21, 6874-6881.  
11864608 T.L.Hendrickson, T.K.Nomanbhoy, Crécy-Lagard, S.Fukai, O.Nureki, S.Yokoyama, and P.Schimmel (2002).
Mutational separation of two pathways for editing by a class I tRNA synthetase.
  Mol Cell, 9, 353-362.  
12186547 X.Du, and E.D.Wang (2002).
Discrimination of tRNA(Leu) isoacceptors by the mutants of Escherichia coli leucyl-tRNA synthetase in editing.
  Biochemistry, 41, 10623-10628.  
12427973 X.L.Yang, R.J.Skene, D.E.McRee, and P.Schimmel (2002).
Crystal structure of a human aminoacyl-tRNA synthetase cytokine.
  Proc Natl Acad Sci U S A, 99, 15369-15374.
PDB code: 1n3l
12186549 Y.Tang, and D.A.Tirrell (2002).
Attenuation of the editing activity of the Escherichia coli leucyl-tRNA synthetase allows incorporation of novel amino acids into proteins in vivo.
  Biochemistry, 41, 10635-10645.  
11698642 A.Shimada, O.Nureki, M.Goto, S.Takahashi, and S.Yokoyama (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.
PDB codes: 1iq0 1ir4
11284704 M.A.Farrow, and P.Schimmel (2001).
Editing by a tRNA synthetase: DNA aptamer-induced translocation and hydrolysis of a misactivated amino acid.
  Biochemistry, 40, 4478-4483.  
  11375928 M.Ibba, and D.Söll (2001).
The renaissance of aminoacyl-tRNA synthesis.
  EMBO Rep, 2, 382-387.  
11166571 M.V.Rodnina, and W.Wintermeyer (2001).
Ribosome fidelity: tRNA discrimination, proofreading and induced fit.
  Trends Biochem Sci, 26, 124-130.  
12762019 O.Nureki, S.Fukai, S.Sekine, A.Shimada, T.Terada, T.Nakama, M.Shirouzu, D.G.Vassylyev, and S.Yokoyama (2001).
Structural basis for amino acid and tRNA recognition by class I aminoacyl-tRNA synthetases.
  Cold Spring Harb Symp Quant Biol, 66, 167-173.  
11331000 R.S.Mursinna, T.L.Lincecum, and S.A.Martinis (2001).
A conserved threonine within Escherichia coli leucyl-tRNA synthetase prevents hydrolytic editing of leucyl-tRNALeu.
  Biochemistry, 40, 5376-5381.  
11412966 T.K.Nomanbhoy, and P.Schimmel (2001).
Active site of an aminoacyl-tRNA synthetase dissected by energy-transfer-dependent fluorescence.
  Bioorg Med Chem Lett, 11, 1485-1491.  
11717415 T.L.Hendrickson (2001).
Recognizing the D-loop of transfer RNAs.
  Proc Natl Acad Sci U S A, 98, 13473-13475.  
11250906 Y.W.Cheng, L.M.Visomirski-Robic, and J.M.Gott (2001).
Non-templated addition of nucleotides to the 3' end of nascent RNA during RNA editing in Physarum.
  EMBO J, 20, 1405-1414.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
10771445 A.Yaremchuk, S.Cusack, O.Gudzera, M.Grøtli, and M.Tukalo (2000).
Crystallization and preliminary crystallographic analysis of Thermus thermophilus leucyl-tRNA synthetase and its complexes with leucine and a non-hydrolysable leucyl-adenylate analogue.
  Acta Crystallogr D Biol Crystallogr, 56, 667-669.  
11060012 B.Delagoutte, D.Moras, and J.Cavarelli (2000).
tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
  EMBO J, 19, 5599-5610.
PDB codes: 1f7u 1f7v
10739930 B.Delagoutte, G.Keith, D.Moras, and J.Cavarelli (2000).
Crystallization and preliminary X-ray crystallographic analysis of yeast arginyl-tRNA synthetase-yeast tRNAArg complexes.
  Acta Crystallogr D Biol Crystallogr, 56, 492-494.  
10903513 C.Hountondji, C.Beauvallet, P.Dessen, C.Hoang-Naudin, J.M.Schmitter, J.C.Pernollet, and S.Blanquet (2000).
Valyl-tRNA synthetase from Escherichia coli MALDI-MS identification of the binding sites for L-valine or for noncognate amino acids upon qualitative comparative labeling with reactive amino-acid analogs.
  Eur J Biochem, 267, 4789-4798.  
11087829 F.Houman, S.B.Rho, J.Zhang, X.Shen, C.C.Wang, P.Schimmel, and S.A.Martinis (2000).
A prokaryote and human tRNA synthetase provide an essential RNA splicing function in yeast mitochondria.
  Proc Natl Acad Sci U S A, 97, 13743-13748.  
10673435 I.Sugiura, O.Nureki, Y.Ugaji-Yoshikawa, S.Kuwabara, A.Shimada, M.Tateno, B.Lorber, R.Giegé, D.Moras, S.Yokoyama, and M.Konno (2000).
The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules.
  Structure, 8, 197-208.
PDB code: 1a8h
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
  Annu Rev Biochem, 69, 617-650.  
10821672 M.J.Brown, L.M.Mensah, M.L.Doyle, N.J.Broom, N.Osbourne, A.K.Forrest, C.M.Richardson, P.J.O'Hanlon, and A.J.Pope (2000).
Rational design of femtomolar inhibitors of isoleucyl tRNA synthetase from a binding model for pseudomonic acid-A.
  Biochemistry, 39, 6003-6011.  
10592262 M.Szymanski, and J.Barciszewski (2000).
Aminoacyl-tRNA synthetases database Y2K.
  Nucleic Acids Res, 28, 326-328.  
10922054 P.J.Beuning, and K.Musier-Forsyth (2000).
Hydrolytic editing by a class II aminoacyl-tRNA synthetase.
  Proc Natl Acad Sci U S A, 97, 8916-8920.  
10744027 R.Geslain, F.Martin, B.Delagoutte, J.Cavarelli, J.Gangloff, and G.Eriani (2000).
In vivo selection of lethal mutations reveals two functional domains in arginyl-tRNA synthetase.
  RNA, 6, 434-448.  
10679458 S.Blanquet, Y.Mechulam, and E.Schmitt (2000).
The many routes of bacterial transfer RNAs after aminoacylation.
  Curr Opin Struct Biol, 10, 95.  
10811626 S.Cusack, A.Yaremchuk, and M.Tukalo (2000).
The 2 A crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue.
  EMBO J, 19, 2351-2361.
PDB code: 1h3n
11105758 T.A.Nissan, and J.J.Perona (2000).
Alternative designs for construction of the class II transfer RNA tertiary core.
  RNA, 6, 1585-1596.  
10792042 T.K.Nomanbhoy, and P.R.Schimmel (2000).
Misactivated amino acids translocate at similar rates across surface of a tRNA synthetase.
  Proc Natl Acad Sci U S A, 97, 5119-5122.  
10889024 T.L.Hendrickson, T.K.Nomanbhoy, and P.Schimmel (2000).
Errors from selective disruption of the editing center in a tRNA synthetase.
  Biochemistry, 39, 8180-8186.  
10549284 T.K.Nomanbhoy, T.L.Hendrickson, and P.Schimmel (1999).
Transfer RNA-dependent translocation of misactivated amino acids to prevent errors in protein synthesis.
  Mol Cell, 4, 519-528.  
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