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PDBsum entry 1qf6

Go to PDB code: 
protein dna_rna ligands metals links
Ligase/RNA PDB id
1qf6
Jmol
Contents
Protein chain
641 a.a. *
DNA/RNA
Ligands
AMP
Metals
_ZN
Waters ×244
* Residue conservation analysis
PDB id:
1qf6
Name: Ligase/RNA
Title: Structure of e. Coli threonyl-tRNA synthetase complexed with cognate tRNA
Structure: Threonine tRNA. Chain: b. Synonym: tRNA (thr). Other_details: complexed with adenosine monophosphate. Threonyl-tRNA synthetase. Chain: a. Synonym: thrrs. Ec: 6.1.1.3
Source: Escherichia coli. Organism_taxid: 562. Organism_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.90Å     R-factor:   0.195     R-free:   0.239
Authors: R.Sankaranarayanan,A.C.Dock-Bregeon,B.Rees,D.Moras
Key ref:
R.Sankaranarayanan et al. (1999). The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell, 97, 371-381. PubMed id: 10319817 DOI: 10.1016/S0092-8674(00)80746-1
Date:
06-Apr-99     Release date:   06-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A8M3  (SYT_ECOLI) -  Threonine--tRNA ligase
Seq:
Struc:
 
Seq:
Struc:
642 a.a.
641 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.3  - Threonine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr)
ATP
+ L-threonine
+ tRNA(Thr)
=
AMP
Bound ligand (Het Group name = AMP)
corresponds exactly
+ diphosphate
+ L-threonyl-tRNA(Thr)
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     regulation of translation   6 terms 
  Biochemical function     nucleotide binding     12 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0092-8674(00)80746-1 Cell 97:371-381 (1999)
PubMed id: 10319817  
 
 
The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site.
R.Sankaranarayanan, A.C.Dock-Bregeon, P.Romby, J.Caillet, M.Springer, B.Rees, C.Ehresmann, B.Ehresmann, D.Moras.
 
  ABSTRACT  
 
E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. The Structure of ThrRS from E. coli(A) A view along the 2-fold axis with the dimer and the tRNAs in CPK representation. The monomers are shown in green and yellow and the corresponding tRNAs in red and violet. The view highlights the CCA ends entering the catalytic core and the cross-subunit contacts.(B) Domain architecture of a monomer of ThrRS. The same color code is used throughout for the different domains. The figure was made using SETOR ([16]).
Figure 4.
Figure 4. Acceptor Arm Recognition(A) CCA interactions in the active site domain. Motifs 2 and 3 are colored in red and green, respectively. The CCA and the protein residues interacting with it are in stick representation. The AMP, the zinc, and a water molecule are represented in orange stick, pink, and cyan spheres, respectively.(B) Minor groove recognition at the acceptor stem. The base-specific interactions are indicated. The phosphate backbone of the tRNA is shown as a purple ribbon where a stick model represents the bases. The interacting residues from the N2 domain are indicated in stick representation.(C) Sequence comparison with AlaRS for the N2 domain. TRSEc represents ThrRS from Escherichia coli, and ARSEc, ARSTt, ARSSc, and ARSHs represent AlaRS from Escherichia coli, Thermus thermophilus, Saccharomyces cerevisiae, and Homo sapiens, respectively. The highly conserved residues in ThrRS and AlaRS surrounding a cleft are indicated by red spheres. (A) and (B) were made using SETOR ([16]) and (C) was made using ALSCRIPT ( [2]).
 
  The above figures are reprinted by permission from Cell Press: Cell (1999, 97, 371-381) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23263184 H.Zhou, L.Sun, X.L.Yang, and P.Schimmel (2013).
ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase.
  Nature, 494, 121-124.
PDB code: 4hvc
21222438 A.Minajigi, B.Deng, and C.S.Francklyn (2011).
Fidelity escape by the unnatural amino acid β-hydroxynorvaline: an efficient substrate for Escherichia coli threonyl-tRNA synthetase with toxic effects on growth.
  Biochemistry, 50, 1101-1109.  
21552257 J.A.Cruz, and E.Westhof (2011).
Sequence-based identification of 3D structural modules in RNA with RMDetect.
  Nat Methods, 8, 513-519.  
20132829 E.A.Merritt, T.L.Arakaki, J.R.Gillespie, E.T.Larson, A.Kelley, N.Mueller, A.J.Napuli, J.Kim, L.Zhang, C.L.Verlinde, E.Fan, F.Zucker, F.S.Buckner, W.C.van Voorhis, and W.G.Hol (2010).
Crystal structures of trypanosomal histidyl-tRNA synthetase illuminate differences between eukaryotic and prokaryotic homologs.
  J Mol Biol, 397, 481-494.
PDB codes: 3hri 3hrk 3lc0
20037152 S.Hou, L.E.Vigeland, G.Zhang, R.Xu, M.Li, S.H.Heinemann, and T.Hoshi (2010).
Zn2+ activates large conductance Ca2+-activated K+ channel via an intracellular domain.
  J Biol Chem, 285, 6434-6442.  
19098308 G.Sharma, and E.A.First (2009).
Thermodynamic Analysis Reveals a Temperature-dependent Change in the Catalytic Mechanism of Bacillus stearothermophilus Tyrosyl-tRNA Synthetase.
  J Biol Chem, 284, 4179-4190.  
19379069 J.Ling, N.Reynolds, and M.Ibba (2009).
Aminoacyl-tRNA synthesis and translational quality control.
  Annu Rev Microbiol, 63, 61-78.  
19247443 K.Morohashi, and E.Grotewold (2009).
A systems approach reveals regulatory circuitry for Arabidopsis trichome initiation by the GL3 and GL1 selectors.
  PLoS Genet, 5, e1000396.  
19118381 K.Nozawa, P.O'Donoghue, S.Gundllapalli, Y.Araiso, R.Ishitani, T.Umehara, D.Söll, and O.Nureki (2009).
Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality.
  Nature, 457, 1163-1167.
PDB codes: 2zni 2znj
19661429 M.Guo, Y.E.Chong, K.Beebe, R.Shapiro, X.L.Yang, and P.Schimmel (2009).
The C-Ala domain brings together editing and aminoacylation functions on one tRNA.
  Science, 325, 744-747.
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.
  Proc Natl Acad Sci U S A, 106, 8489-8494.
PDB codes: 2ztg 2zvf
19385727 P.Babitzke, C.S.Baker, and T.Romeo (2009).
Regulation of translation initiation by RNA binding proteins.
  Annu Rev Microbiol, 63, 27-44.  
19710017 R.T.Guo, Y.E.Chong, M.Guo, and X.L.Yang (2009).
Crystal structures and biochemical analyses suggest a unique mechanism and role for human glycyl-tRNA synthetase in Ap4A homeostasis.
  J Biol Chem, 284, 28968-28976.  
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.  
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.
  Biochemistry, 47, 13326-13335.
PDB code: 3c8z
18160411 N.J.Reiter, L.J.Maher, and S.E.Butcher (2008).
DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.
  Nucleic Acids Res, 36, 1227-1236.
PDB code: 2jwv
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.  
18384044 S.Goto-Ito, T.Ito, R.Ishii, Y.Muto, Y.Bessho, and S.Yokoyama (2008).
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
  Proteins, 72, 1274-1289.
PDB code: 2yx1
  18931432 S.Shimizu, E.C.Juan, Y.I.Miyashita, Y.Sato, M.M.Hoque, K.Suzuki, M.Yogiashi, M.Tsunoda, A.C.Dock-Bregeon, D.Moras, T.Sekiguchi, and A.Takénaka (2008).
Crystallization and preliminary crystallographic studies of putative threonyl-tRNA synthetases from Aeropyrum pernix and Sulfolobus tokodaii.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 903-910.  
17605815 A.M.Burroughs, S.Balaji, L.M.Iyer, and L.Aravind (2007).
Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.
  Biol Direct, 2, 18.  
17384228 C.W.Kim, K.S.Han, K.S.Ryu, B.H.Kim, K.H.Kim, S.I.Choi, and B.L.Seong (2007).
N-terminal domains of native multidomain proteins have the potential to assist de novo folding of their downstream domains in vivo by acting as solubility enhancers.
  Protein Sci, 16, 635-643.  
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.  
17644600 J.Caillet, M.Graffe, F.Eyermann, P.Romby, and M.Springer (2007).
Mutations in residues involved in zinc binding in the catalytic site of Escherichia coli threonyl-tRNA synthetase confer a dominant lethal phenotype.
  J Bacteriol, 189, 6839-6848.  
17185419 J.Ling, H.Roy, and M.Ibba (2007).
Mechanism of tRNA-dependent editing in translational quality control.
  Proc Natl Acad Sci U S A, 104, 72-77.  
17283340 J.SternJohn, S.Hati, P.G.Siliciano, and K.Musier-Forsyth (2007).
Restoring species-specific posttransfer editing activity to a synthetase with a defunct editing domain.
  Proc Natl Acad Sci U S A, 104, 2127-2132.  
17595294 L.A.Nangle, W.Zhang, W.Xie, X.L.Yang, and P.Schimmel (2007).
Charcot-Marie-Tooth disease-associated mutant tRNA synthetases linked to altered dimer interface and neurite distribution defect.
  Proc Natl Acad Sci U S A, 104, 11239-11244.  
18020710 M.Hiller, Z.Zhang, R.Backofen, and S.Stamm (2007).
Pre-mRNA Secondary Structures Influence Exon Recognition.
  PLoS Genet, 3, e204.  
17327676 R.Fukunaga, and S.Yokoyama (2007).
Structure of the AlaX-M trans-editing enzyme from Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 63, 390-400.
PDB code: 2e1b
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17078815 A.Battesti, and E.Bouveret (2006).
Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism.
  Mol Microbiol, 62, 1048-1063.  
17188032 C.Hoang, J.Chen, C.A.Vizthum, J.M.Kandel, C.S.Hamilton, E.G.Mueller, and A.R.Ferré-D'Amaré (2006).
Crystal structure of pseudouridine synthase RluA: indirect sequence readout through protein-induced RNA structure.
  Mol Cell, 24, 535-545.
PDB code: 2i82
16374837 J.Ishijima, Y.Uchida, C.Kuroishi, C.Tuzuki, N.Takahashi, N.Okazaki, K.Yutani, and M.Miyano (2006).
Crystal structure of alanyl-tRNA synthetase editing-domain homolog (PH0574) from a hyperthermophile, Pyrococcus horikoshii OT3 at 1.45 A resolution.
  Proteins, 62, 1133-1137.
PDB code: 1v4p
17015650 K.Kasai, T.Nishizawa, K.Takahashi, T.Hosaka, H.Aoki, and K.Ochi (2006).
Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus.
  J Bacteriol, 188, 7111-7122.  
16859499 L.M.Iyer, A.M.Burroughs, and L.Aravind (2006).
The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.
  Genome Biol, 7, R60.  
17041036 L.N.DiDonato, S.A.Sullivan, B.A.Methé, K.P.Nevin, R.England, and D.R.Lovley (2006).
Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens.
  J Bacteriol, 188, 8469-8478.  
16864571 S.Hati, B.Ziervogel, J.Sternjohn, F.C.Wong, M.C.Nagan, A.E.Rosen, P.G.Siliciano, J.W.Chihade, and K.Musier-Forsyth (2006).
Pre-transfer editing by class II prolyl-tRNA synthetase: role of aminoacylation active site in "selective release" of noncognate amino acids.
  J Biol Chem, 281, 27862-27872.  
16731979 V.Jain, R.Saleem-Batcha, A.China, and D.Chatterji (2006).
Molecular dissection of the mycobacterial stringent response protein Rel.
  Protein Sci, 15, 1449-1464.  
15507440 B.Ruan, M.L.Bovee, M.Sacher, C.Stathopoulos, K.Poralla, C.S.Francklyn, and D.Söll (2005).
A unique hydrophobic cluster near the active site contributes to differences in borrelidin inhibition among threonyl-tRNA synthetases.
  J Biol Chem, 280, 571-577.  
16059752 H.L.Wu, S.Bagby, and J.M.van den Elsen (2005).
Evolution of the genetic triplet code via two types of doublet codons.
  J Mol Evol, 61, 54-64.  
16087889 M.Sokabe, A.Okada, M.Yao, T.Nakashima, and I.Tanaka (2005).
Molecular basis of alanine discrimination in editing site.
  Proc Natl Acad Sci U S A, 102, 11669-11674.
PDB codes: 1v7o 1wnu 1wxo
15562516 N.Rekha, S.M.Machado, C.Narayanan, A.Krupa, and N.Srinivasan (2005).
Interaction interfaces of protein domains are not topologically equivalent across families within superfamilies: Implications for metabolic and signaling pathways.
  Proteins, 58, 339-353.  
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.
  Proc Natl Acad Sci U S A, 101, 10260-10265.  
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.
  EMBO J, 23, 4639-4648.  
14997565 K.W.Lee, and J.M.Briggs (2004).
Molecular modeling study of the editing active site of Escherichia coli leucyl-tRNA synthetase: two amino acid binding sites in the editing domain.
  Proteins, 54, 693-704.  
14764088 R.Banerjee, D.Y.Dubois, J.Gauthier, S.X.Lin, S.Roy, and J.Lapointe (2004).
The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that modulates amino acid binding via the tRNA acceptor arm.
  Eur J Biochem, 271, 724-733.  
15487945 R.Finking, and M.A.Marahiel (2004).
Biosynthesis of nonribosomal peptides1.
  Annu Rev Microbiol, 58, 453-488.  
15333948 S.Dwivedi, S.P.Kruparani, and R.Sankaranarayanan (2004).
Cloning, expression, purification, crystallization and preliminary X-ray crystallographic investigations of a unique editing domain from archaebacteria.
  Acta Crystallogr D Biol Crystallogr, 60, 1662-1664.  
12837776 A.Teplyakov, G.Obmolova, S.Y.Chu, J.Toedt, E.Eisenstein, A.J.Howard, and G.L.Gilliland (2003).
Crystal structure of the YchF protein reveals binding sites for GTP and nucleic acid.
  J Bacteriol, 185, 4031-4037.
PDB code: 1jal
12761395 D.Tworowski, and M.Safro (2003).
The long-range electrostatic interactions control tRNA-aminoacyl-tRNA synthetase complex formation.
  Protein Sci, 12, 1247-1251.  
12773376 H.J.Ahn, H.W.Kim, H.J.Yoon, B.I.Lee, S.W.Suh, and J.K.Yang (2003).
Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition.
  EMBO J, 22, 2593-2603.
PDB codes: 1uaj 1uak 1ual 1uam
12824344 H.Yang, F.Jossinet, N.Leontis, L.Chen, J.Westbrook, H.Berman, and E.Westhof (2003).
Tools for the automatic identification and classification of RNA base pairs.
  Nucleic Acids Res, 31, 3450-3460.  
14663147 I.Ahel, D.Korencic, M.Ibba, and D.Söll (2003).
Trans-editing of mischarged tRNAs.
  Proc Natl Acad Sci U S A, 100, 15422-15427.  
12581352 J.Caillet, T.Nogueira, B.Masquida, F.Winter, M.Graffe, A.C.Dock-Brégeon, A.Torres-Larios, R.Sankaranarayanan, E.Westhof, B.Ehresmann, C.Ehresmann, P.Romby, and M.Springer (2003).
The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression.
  Mol Microbiol, 47, 961-974.  
12554667 K.Beebe, L.Ribas De Pouplana, and P.Schimmel (2003).
Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability.
  EMBO J, 22, 668-675.  
12837795 L.Volpon, C.Lievre, M.J.Osborne, S.Gandhi, P.Iannuzzi, R.Larocque, M.Cygler, K.Gehring, and I.Ekiel (2003).
The solution structure of YbcJ from Escherichia coli reveals a recently discovered alphaL motif involved in RNA binding.
  J Bacteriol, 185, 4204-4210.
PDB codes: 1o09 1p9k
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.
  Biochemistry, 42, 15102-15113.  
12787346 P.J.Schlax, and D.J.Worhunsky (2003).
Translational repression mechanisms in prokaryotes.
  Mol Microbiol, 48, 1157-1169.  
12615010 P.Romby, and M.Springer (2003).
Bacterial translational control at atomic resolution.
  Trends Genet, 19, 155-161.  
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.  
12165569 F.J.Grundy, W.C.Winkler, and T.M.Henkin (2002).
tRNA-mediated transcription antitermination in vitro: codon-anticodon pairing independent of the ribosome.
  Proc Natl Acad Sci U S A, 99, 11121-11126.  
12379656 J.A.Carrodeguas, K.G.Pinz, and D.F.Bogenhagen (2002).
DNA binding properties of human pol gammaB.
  J Biol Chem, 277, 50008-50014.  
11604396 J.A.Tanner, A.Abowath, and A.D.Miller (2002).
Isothermal titration calorimetry reveals a zinc ion as an atomic switch in the diadenosine polyphosphates.
  J Biol Chem, 277, 3073-3078.  
12005430 J.I.Guijarro, A.Pintar, A.Prochnicka-Chalufour, V.Guez, B.Gilquin, H.Bedouelle, and M.Delepierre (2002).
Structure and dynamics of the anticodon arm binding domain of Bacillus stearothermophilus Tyrosyl-tRNA synthetase.
  Structure, 10, 311-317.
PDB code: 1jh3
11953756 J.Sivaraman, V.Sauvé, R.Larocque, E.A.Stura, J.D.Schrag, M.Cygler, and A.Matte (2002).
Structure of the 16S rRNA pseudouridine synthase RsuA bound to uracil and UMP.
  Nat Struct Biol, 9, 353-358.
PDB codes: 1ksk 1ksl 1ksv
12392550 K.Ye, A.Serganov, W.Hu, M.Garber, and D.J.Patel (2002).
Ribosome-associated factor Y adopts a fold resembling a double-stranded RNA binding domain scaffold.
  Eur J Biochem, 269, 5182-5191.
PDB code: 1l4s
12022232 P.J.Beuning, M.C.Nagan, C.J.Cramer, K.Musier-Forsyth, J.L.Gelpí, and D.Bashford (2002).
Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.
  RNA, 8, 659-670.  
12019264 T.Takita, and K.Inouye (2002).
Transition state stabilization by the N-terminal anticodon-binding domain of lysyl-tRNA synthetase.
  J Biol Chem, 277, 29275-29282.  
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
11435117 H.A.Lewis, E.B.Furlong, B.Laubert, G.A.Eroshkina, Y.Batiyenko, J.M.Adams, M.G.Bergseid, C.D.Marsh, T.S.Peat, W.E.Sanderson, J.M.Sauder, and S.G.Buchanan (2001).
A structural genomics approach to the study of quorum sensing: crystal structures of three LuxS orthologs.
  Structure, 9, 527-537.
PDB codes: 1inn 1j6v 1j6w 1j6x 1vje
11172710 J.A.Carrodeguas, K.Theis, D.F.Bogenhagen, and C.Kisker (2001).
Crystal structure and deletion analysis show that the accessory subunit of mammalian DNA polymerase gamma, Pol gamma B, functions as a homodimer.
  Mol Cell, 7, 43-54.
PDB codes: 1g5h 1g5i
11269237 L.Ribas de Pouplana, and P.Schimmel (2001).
Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem.
  Cell, 104, 191-193.  
11590011 L.Ribas de Pouplana, and P.Schimmel (2001).
Aminoacyl-tRNA synthetases: potential markers of genetic code development.
  Trends Biochem Sci, 26, 591-596.  
11553770 M.T.Hilgers, and M.L.Ludwig (2001).
Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.
  Proc Natl Acad Sci U S A, 98, 11169-11174.
PDB code: 1ie0
11679717 R.Fishman, V.Ankilova, N.Moor, and M.Safro (2001).
Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.
  Acta Crystallogr D Biol Crystallogr, 57, 1534-1544.
PDB code: 1jjc
11329259 S.A.Hawko, and C.S.Francklyn (2001).
Covariation of a specificity-determining structural motif in an aminoacyl-tRNA synthetase and a tRNA identity element.
  Biochemistry, 40, 1930-1936.  
10679466 A.A.Antson (2000).
Single-stranded-RNA binding proteins.
  Curr Opin Struct Biol, 10, 87-94.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
10970866 A.Yaremchuk, S.Cusack, and M.Tukalo (2000).
Crystal structure of a eukaryote/archaeon-like protyl-tRNA synthetase and its complex with tRNAPro(CGG).
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11112540 B.Burke, F.Yang, F.Chen, C.Stehlin, B.Chan, and K.Musier-Forsyth (2000).
Evolutionary coadaptation of the motif 2--acceptor stem interaction in the class II prolyl-tRNA synthetase system.
  Biochemistry, 39, 15540-15547.  
11060012 B.Delagoutte, D.Moras, and J.Cavarelli (2000).
tRNA aminoacylation by arginyl-tRNA synthetase: induced conformations during substrates binding.
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PDB codes: 1f7u 1f7v
10675344 B.L.Staker, P.Korber, J.C.Bardwell, and M.A.Saper (2000).
Structure of Hsp15 reveals a novel RNA-binding motif.
  EMBO J, 19, 749-757.
PDB code: 1dm9
10710420 C.S.Chiang, and G.J.Liaw (2000).
A missense mutation in the nuclear gene coding for the mitochondrial aspartyl-tRNA synthetase suppresses a mitochondrial tRNA(Asp) mutation.
  Nucleic Acids Res, 28, 1542-1547.  
10745012 E.Westhof, and V.Fritsch (2000).
RNA folding: beyond Watson-Crick pairs.
  Structure, 8, R55-R65.  
10841541 G.Minasov, M.Teplova, G.C.Stewart, E.V.Koonin, W.F.Anderson, and M.Egli (2000).
Functional implications from crystal structures of the conserved Bacillus subtilis protein Maf with and without dUTP.
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PDB codes: 1ex2 1exc
10678983 G.Subramanian, E.V.Koonin, and L.Aravind (2000).
Comparative genome analysis of the pathogenic spirochetes Borrelia burgdorferi and Treponema pallidum.
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10676814 H.A.Lewis, K.Musunuru, K.B.Jensen, C.Edo, H.Chen, R.B.Darnell, and S.K.Burley (2000).
Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.
  Cell, 100, 323-332.
PDB code: 1ec6
10813833 H.Zhang, K.Huang, Z.Li, L.Banerjei, K.E.Fisher, N.V.Grishin, E.Eisenstein, and O.Herzberg (2000).
Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.
  Proteins, 40, 86-97.
PDB codes: 1dbu 1dbx
10889033 J.A.Pleiss, A.D.Wolfson, and O.C.Uhlenbeck (2000).
Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule.
  Biochemistry, 39, 8250-8258.  
10966471 M.Ibba, and D.Soll (2000).
Aminoacyl-tRNA synthesis.
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11118226 M.Kaminska, M.Deniziak, P.Kerjan, J.Barciszewski, and M.Mirande (2000).
A recurrent general RNA binding domain appended to plant methionyl-tRNA synthetase acts as a cis-acting cofactor for aminoacylation.
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10592262 M.Szymanski, and J.Barciszewski (2000).
Aminoacyl-tRNA synthetases database Y2K.
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11041850 S.Onesti, G.Desogus, A.Brevet, J.Chen, P.Plateau, S.Blanquet, and P.Brick (2000).
Structural studies of lysyl-tRNA synthetase: conformational changes induced by substrate binding.
  Biochemistry, 39, 12853-12861.
PDB codes: 1bbu 1bbw
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.  
10632708 V.Cura, D.Moras, and D.Kern (2000).
Sequence analysis and modular organization of threonyl-tRNA synthetase from Thermus thermophilus and its interrelation with threonyl-tRNA synthetases of other origins.
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10677223 V.Guez, S.Nair, A.Chaffotte, and H.Bedouelle (2000).
The anticodon-binding domain of tyrosyl-tRNA synthetase: state of folding and origin of the crystallographic disorder.
  Biochemistry, 39, 1739-1747.  
10497122 J.H.Cate, M.M.Yusupov, G.Z.Yusupova, T.N.Earnest, and H.F.Noller (1999).
X-ray crystal structures of 70S ribosome functional complexes.
  Science, 285, 2095-2104.
PDB code: 486d
10518524 K.Y.Chang, G.Varani, S.Bhattacharya, H.Choi, and W.H.McClain (1999).
Correlation of deformability at a tRNA recognition site and aminoacylation specificity.
  Proc Natl Acad Sci U S A, 96, 11764-11769.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
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