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PDBsum entry 1j1u

Go to PDB code: 
protein dna_rna ligands metals links
Ligase/RNA PDB id
1j1u
Jmol
Contents
Protein chain
299 a.a. *
DNA/RNA
Ligands
TYR
Metals
_MG ×4
Waters ×364
* Residue conservation analysis
PDB id:
1j1u
Name: Ligase/RNA
Title: Crystal structure of archaeal tyrosyl-tRNA synthetase complexed with tRNA(tyr) and l-tyrosine
Structure: tRNA(tyr). Chain: b. Engineered: yes. Tyrosyl-tRNA synthetase. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence occurs in methanococcus jannaschii.. Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: tyrs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Tetramer (from PDB file)
Resolution:
1.95Å     R-factor:   0.188     R-free:   0.239
Authors: T.Kobayashi,O.Nureki,R.Ishitani,M.Tukalo,S.Cusack, K.Sakamoto,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Kobayashi et al. (2003). Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion. Nat Struct Biol, 10, 425-432. PubMed id: 12754495 DOI: 10.1038/nsb934
Date:
17-Dec-02     Release date:   03-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q57834  (SYY_METJA) -  Tyrosine--tRNA ligase
Seq:
Struc:
306 a.a.
299 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.1.1.1  - Tyrosine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
ATP
+
L-tyrosine
Bound ligand (Het Group name = TYR)
corresponds exactly
+ tRNA(Tyr)
= AMP
+ diphosphate
+ L-tyrosyl-tRNA(Tyr)
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  

 

 
    reference    
 
 
DOI no: 10.1038/nsb934 Nat Struct Biol 10:425-432 (2003)
PubMed id: 12754495  
 
 
Structural basis for orthogonal tRNA specificities of tyrosyl-tRNA synthetases for genetic code expansion.
T.Kobayashi, O.Nureki, R.Ishitani, A.Yaremchuk, M.Tukalo, S.Cusack, K.Sakamoto, S.Yokoyama.
 
  ABSTRACT  
 
The archaeal/eukaryotic tyrosyl-tRNA synthetase (TyrRS)-tRNA(Tyr) pairs do not cross-react with their bacterial counterparts. This 'orthogonal' condition is essential for using the archaeal pair to expand the bacterial genetic code. In this study, the structure of the Methanococcus jannaschii TyrRS-tRNA(Tyr)-L-tyrosine complex, solved at a resolution of 1.95 A, reveals that this archaeal TyrRS strictly recognizes the C1-G72 base pair, whereas the bacterial TyrRS recognizes the G1-C72 in a different manner using different residues. These diverse tRNA recognition modes form the basis for the orthogonality. The common tRNA(Tyr) identity determinants (the discriminator, A73 and the anticodon residues) are also recognized in manners different from those of the bacterial TyrRS. Based on this finding, we created a mutant TyrRS that aminoacylates the amber suppressor tRNA with C34 65 times more efficiently than does the wild-type enzyme.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Comparison of the overall structures of TyrRSs. (a) Stereo view of the superimposed TyrRS -tRNA^Tyr structures from M. jannaschii (red) and T. thermophilus (black; PDB entry 1H3E)28. Only one of the two tRNA^Tyr molecules is shown. (b) Superposition in a as viewed from the long axis of the dimers. The superposition views were produced using LSQKAB^44.
Figure 4.
Figure 4. Acceptor arm recognition by TyrRSs. (a) Stereo view of the acceptor arm -binding site of the M. jannaschii TyrRS. (b) Stereo view around the first base pair of tRNA^Tyr in the M. jannaschii complex. The 5' terminal phosphate in the tRNA^Tyr is missing because the tRNA was produced by self-cleavage of a 'transzyme'40 transcribed in vitro (see Methods). (c) The corresponding stereo view of the T. thermophilus complex. In b and c, nucleotides 1, 72 and 73 in each tRNA^Tyr are shown as stick models. The carbon atoms of the tRNAs and the nitrogen, oxygen, phosphorus and sulfur atoms are shown in yellow, blue, red, green and brown, respectively. Hydrogen bonds are indicated by red broken lines. In the ribbon models, the N-terminal region, the Rossmann-fold domain, and the CP1 domain are colored as in Fig. 1b.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 425-432) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22683997 A.Palencia, T.Crépin, M.T.Vu, T.L.Lincecum, S.A.Martinis, and S.Cusack (2012).
Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase.
  Nat Struct Mol Biol, 19, 677-684.
PDB codes: 4aq7 4arc 4ari 4as1
21224416 A.K.Antonczak, Z.Simova, I.T.Yonemoto, M.Bochtler, A.Piasecka, H.Czapinska, A.Brancale, and E.M.Tippmann (2011).
Importance of single molecular determinants in the fidelity of expanded genetic codes.
  Proc Natl Acad Sci U S A, 108, 1320-1325.
PDB code: 3prh
20307192 C.C.Liu, and P.G.Schultz (2010).
Adding new chemistries to the genetic code.
  Annu Rev Biochem, 79, 413-444.  
20796028 H.Ingvarsson, and T.Unge (2010).
Flexibility and communication within the structure of the Mycobacterium smegmatis methionyl-tRNA synthetase.
  FEBS J, 277, 3947-3962.
PDB codes: 2x1l 2x1m
20217843 I.T.Yonemoto, and E.M.Tippmann (2010).
The juggernauts of biology.
  Bioessays, 32, 314-321.  
20852636 M.W.Vetting, S.S.Hegde, and J.S.Blanchard (2010).
The structure and mechanism of the Mycobacterium tuberculosis cyclodityrosine synthetase.
  Nat Chem Biol, 6, 797-799.
PDB code: 2x9q
20689681 N.B.Ulyanov, and T.L.James (2010).
RNA structural motifs that entail hydrogen bonds involving sugar-phosphate backbone atoms of RNA.
  New J Chem, 34, 910-917.  
19666472 A.K.Antonczak, Z.Simova, and E.M.Tippmann (2009).
A critical examination of Escherichia coli esterase activity.
  J Biol Chem, 284, 28795-28800.  
19668857 J.K.Takimoto, K.L.Adams, Z.Xiang, and L.Wang (2009).
Improving orthogonal tRNA-synthetase recognition for efficient unnatural amino acid incorporation and application in mammalian cells.
  Mol Biosyst, 5, 931-934.  
19278648 K.Sakamoto, K.Murayama, K.Oki, F.Iraha, M.Kato-Murayama, M.Takahashi, K.Ohtake, T.Kobayashi, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2009).
Genetic encoding of 3-iodo-L-tyrosine in Escherichia coli for single-wavelength anomalous dispersion phasing in protein crystallography.
  Structure, 17, 335-344.
PDB codes: 2z0z 2z10 2zxv
19386777 S.Kamijo, A.Fujii, K.Onodera, and K.Wakabayashi (2009).
Analyses of conditions for KMSSS loop in tyrosyl-tRNA synthetase by building a mutant library.
  J Biochem, 146, 241-250.  
18824174 E.J.Drake, and A.M.Gulick (2008).
Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin.
  J Mol Biol, 384, 193-205.
PDB codes: 3e59 3eat
18268021 L.Bonnefond, C.Florentz, R.Giegé, and J.Rudinger-Thirion (2008).
Decreased aminoacylation in pathology-related mutants of mitochondrial tRNATyr is associated with structural perturbations in tRNA architecture.
  RNA, 14, 641-648.  
18451863 L.Randau, I.Schröder, and D.Söll (2008).
Life without RNase P.
  Nature, 453, 120-123.  
18576636 S.E.Cellitti, D.H.Jones, L.Lagpacan, X.Hao, Q.Zhang, H.Hu, S.M.Brittain, A.Brinker, J.Caldwell, B.Bursulaya, G.Spraggon, A.Brock, Y.Ryu, T.Uno, P.G.Schultz, and B.H.Geierstanger (2008).
In vivo incorporation of unnatural amino acids to probe structure, dynamics, and ligand binding in a large protein by nuclear magnetic resonance spectroscopy.
  J Am Chem Soc, 130, 9268-9281.  
18560823 T.Li, M.Froeyen, and P.Herdewijn (2008).
Comparative structural dynamics of Tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics.
  Eur Biophys J, 38, 25-35.  
18623072 Z.Gáspári, G.Pál, and A.Perczel (2008).
A redesigned genetic code for selective labeling in protein NMR.
  Bioessays, 30, 772-780.  
17855524 C.Abergel, J.Rudinger-Thirion, R.Giegé, and J.M.Claverie (2007).
Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS.
  J Virol, 81, 12406-12417.
PDB code: 2j5b
18000916 E.M.Tippmann, W.Liu, D.Summerer, A.V.Mack, and P.G.Schultz (2007).
A genetically encoded diazirine photocrosslinker in Escherichia coli.
  Chembiochem, 8, 2210-2214.
PDB codes: 2q1g 2q1i 3d6u 3d6v
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.  
17576676 M.Tsunoda, Y.Kusakabe, N.Tanaka, S.Ohno, M.Nakamura, T.Senda, T.Moriguchi, N.Asai, M.Sekine, T.Yokogawa, K.Nishikawa, and K.T.Nakamura (2007).
Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms.
  Nucleic Acids Res, 35, 4289-4300.
PDB code: 2dlc
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17637340 X.L.Yang, M.Guo, M.Kapoor, K.L.Ewalt, F.J.Otero, R.J.Skene, D.E.McRee, and P.Schimmel (2007).
Functional and crystal structure analysis of active site adaptations of a potent anti-angiogenic human tRNA synthetase.
  Structure, 15, 793-805.
PDB code: 1r6u
16548032 A.Deiters, D.Groff, Y.Ryu, J.Xie, and P.G.Schultz (2006).
A genetically encoded photocaged tyrosine.
  Angew Chem Int Ed Engl, 45, 2728-2731.  
16618920 J.M.Turner, J.Graziano, G.Spraggon, and P.G.Schultz (2006).
Structural plasticity of an aminoacyl-tRNA synthetase active site.
  Proc Natl Acad Sci U S A, 103, 6483-6488.
PDB codes: 1zh0 2ag6
16926858 J.Xie, and P.G.Schultz (2006).
A chemical toolkit for proteins--an expanded genetic code.
  Nat Rev Mol Cell Biol, 7, 775-782.  
16689635 L.Wang, J.Xie, and P.G.Schultz (2006).
Expanding the genetic code.
  Annu Rev Biophys Biomol Struct, 35, 225-249.  
17406555 N.Hino, A.Hayashi, K.Sakamoto, and S.Yokoyama (2006).
Site-specific incorporation of non-natural amino acids into proteins in mammalian cells with an expanded genetic code.
  Nat Protoc, 1, 2957-2962.  
16461956 R.Oliva, L.Cavallo, and A.Tramontano (2006).
Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions.
  Nucleic Acids Res, 34, 865-879.  
16724112 X.L.Yang, F.J.Otero, K.L.Ewalt, J.Liu, M.A.Swairjo, C.Köhrer, U.L.RajBhandary, R.J.Skene, D.E.McRee, and P.Schimmel (2006).
Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis.
  EMBO J, 25, 2919-2929.
PDB code: 2azx
16554830 Y.Ryu, and P.G.Schultz (2006).
Efficient incorporation of unnatural amino acids into proteins in Escherichia coli.
  Nat Methods, 3, 263-265.  
16121397 D.Lejeune, N.Delsaux, B.Charloteaux, A.Thomas, and R.Brasseur (2005).
Protein-nucleic acid recognition: statistical analysis of atomic interactions and influence of DNA structure.
  Proteins, 61, 258-271.  
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.  
15840810 L.Bonnefond, M.Frugier, R.Giegé, and J.Rudinger-Thirion (2005).
Human mitochondrial TyrRS disobeys the tyrosine identity rules.
  RNA, 11, 558-562.  
15782189 N.Hino, Y.Okazaki, T.Kobayashi, A.Hayashi, K.Sakamoto, and S.Yokoyama (2005).
Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid.
  Nat Methods, 2, 201-206.  
15671170 T.Kobayashi, K.Sakamoto, T.Takimura, R.Sekine, V.P.Kelly, K.Vincent, K.Kamata, S.Nishimura, and S.Yokoyama (2005).
Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion.
  Proc Natl Acad Sci U S A, 102, 1366-1371.
PDB codes: 1vbn 1wq3 1wq4
16098189 T.Rathinavelan, and N.Yathindra (2005).
Molecular dynamics structures of peptide nucleic acid x DNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene--stereochemical rationale for the low affinity of PNA in the presence of an AC mismatch.
  FEBS J, 272, 4055-4070.  
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
15239046 A.Strømgaard, A.A.Jensen, and K.Strømgaard (2004).
Site-specific incorporation of unnatural amino acids into proteins.
  Chembiochem, 5, 909-916.  
15576346 C.Köhrer, E.L.Sullivan, and U.L.RajBhandary (2004).
Complete set of orthogonal 21st aminoacyl-tRNA synthetase-amber, ochre and opal suppressor tRNA pairs: concomitant suppression of three different termination codons in an mRNA in mammalian cells.
  Nucleic Acids Res, 32, 6200-6211.  
15280378 J.Jia, X.L.Chen, L.T.Guo, Y.D.Yu, J.P.Ding, and Y.X.Jin (2004).
Residues Lys-149 and Glu-153 switch the aminoacylation of tRNA(Trp) in Bacillus subtilis.
  J Biol Chem, 279, 41960-41965.  
15599909 L.Wang, and P.G.Schultz (2004).
Expanding the genetic code.
  Angew Chem Int Ed Engl, 44, 34-66.  
15578784 N.Budisa (2004).
Prolegomena to future experimental efforts on genetic code engineering by expanding its amino acid repertoire.
  Angew Chem Int Ed Engl, 43, 6426-6463.  
15388951 R.Fukunaga, and S.Yokoyama (2004).
Crystallization and preliminary X-ray crystallographic study of leucyl-tRNA synthetase from the archaeon Pyrococcus horikoshii.
  Acta Crystallogr D Biol Crystallogr, 60, 1916-1918.  
14730354 Y.Kise, S.W.Lee, S.G.Park, S.Fukai, T.Sengoku, R.Ishii, S.Yokoyama, S.Kim, and O.Nureki (2004).
A short peptide insertion crucial for angiostatic activity of human tryptophanyl-tRNA synthetase.
  Nat Struct Mol Biol, 11, 149-156.
PDB code: 1ulh
14665676 P.O'Donoghue, and Z.Luthey-Schulten (2003).
On the evolution of structure in aminoacyl-tRNA synthetases.
  Microbiol Mol Biol Rev, 67, 550-573.  
12768199 R.Giegé (2003).
Genetic code expansion.
  Nat Struct Biol, 10, 414-416.  
14671330 X.L.Yang, F.J.Otero, R.J.Skene, D.E.McRee, P.Schimmel, and L.Ribas de Pouplana (2003).
Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains.
  Proc Natl Acad Sci U S A, 100, 15376-15380.
PDB codes: 1q11 1r6t
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.