PDBsum entry 1vbn

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Ligase PDB id
Protein chains
318 a.a. *
YSA ×2
Waters ×115
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Escherichia coli tyrosyl-tRNA synthetase mutant complexed with tyr-ams
Structure: Tyrosyl-tRNA synthetase. Chain: a, b. Fragment: residues 5-322. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PQS)
2.70Å     R-factor:   0.217     R-free:   0.283
Authors: T.Kobayashi,K.Sakamoto,T.Takimura,K.Kamata,R.Sekine, S.Nishimura,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Kobayashi et al. (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. PubMed id: 15671170 DOI: 10.1073/pnas.0407039102
27-Feb-04     Release date:   25-Jan-05    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0AGJ9  (SYY_ECOLI) -  Tyrosine--tRNA ligase
424 a.a.
318 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Tyrosine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-tyrosine + tRNA(Tyr) = AMP + diphosphate + L-tyrosyl-tRNA(Tyr)
+ L-tyrosine
+ tRNA(Tyr)
Bound ligand (Het Group name = YSA)
matches with 48.00% similarity
+ 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     tRNA aminoacylation for protein translation   2 terms 
  Biochemical function     nucleotide binding     4 terms  


DOI no: 10.1073/pnas.0407039102 Proc Natl Acad Sci U S A 102:1366-1371 (2005)
PubMed id: 15671170  
Structural basis of nonnatural amino acid recognition by an engineered aminoacyl-tRNA synthetase for genetic code expansion.
T.Kobayashi, K.Sakamoto, T.Takimura, R.Sekine, V.P.Kelly, K.Vincent, K.Kamata, S.Nishimura, S.Yokoyama.
The genetic code in a eukaryotic system has been expanded by the engineering of Escherichia coli tyrosyl-tRNA synthetase (TyrRS) with the Y37V and Q195C mutations (37V195C), which specifically recognize 3-iodo-L-tyrosine rather than L-tyrosine. In the present study, we determined the 3-iodo-L-tyrosine- and L-tyrosine-bound structures of the 37V195C mutant of the E. coli TyrRS catalytic domain at 2.0-A resolution. The gamma-methyl group of Val-37 and the sulfur atom of Cys-195 make van der Waals contacts with the iodine atom of 3-iodo-L-tyrosine. The Val-37 and Cys-195 side chains are rigidly fixed by the neighboring residues forming the hydrophobic core of the TyrRS. The major roles of the two mutations are different for the 3-iodo-L-tyrosine-selective recognition in the first step of the aminoacylation reaction (the amino acid activation step): the Y37V mutation eliminates the fatal steric repulsion with the iodine atom, and the Q195C mutation reduces the L-tyrosine misrecognition. The structure of the 37V195C mutant TyrRS complexed with an L-tyrosyladenylate analogue was also solved, indicating that the 3-iodo-L-tyrosine and L-tyrosine side chains are similarly discriminated in the second step (the aminoacyl transfer step). These results demonstrate that the amino acid-binding pocket on the 37V195C mutant is optimized for specific 3-iodo-L-tyrosine recognition.
  Selected figure(s)  
Figure 2.
Fig. 2. Comparison of the substrate-binding site structures of E. coli TyrRSs. (A-C) The amino acid-binding site of the wild-type TyrRS·L-tyrosine (A) (19), 37V195C TyrRS·3-iodo-L-tyrosine (B), and 37V195C TyrRS·L-tyrosine (C) complexes. The colors of the atoms are the same as in Fig. 1 C and D. The hydrogen bonds are indicated by pink broken lines. (D) Superposed 37V195C (light blue) and wild-type (green) TyrRS·L-tyrosine structures. The water molecules are shown by balls. The water molecule that hydrogen-bonds to the L-tyrosine is labeled "Wat." (E) Superposed 37V195C mutant TyrRS structures complexed with 3-iodo-L-tyrosine (pink) and L-tyrosine (light blue).
Figure 4.
Fig. 4. Superposed 37V195C (pink) and wild-type (light blue) (19) TyrRS·Tyr-AMS structures. The nitrogen, oxygen, and sulfur atoms are colored blue, red, and yellow, respectively.
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20159998 F.Iraha, K.Oki, T.Kobayashi, S.Ohno, T.Yokogawa, K.Nishikawa, S.Yokoyama, and K.Sakamoto (2010).
Functional replacement of the endogenous tyrosyl-tRNA synthetase-tRNATyr pair by the archaeal tyrosine pair in Escherichia coli for genetic code expansion.
  Nucleic Acids Res, 38, 3682-3691.
PDB code: 2yxn
21127037 G.Kawai, and S.Yokoyama (2010).
Professor Tatsuo Miyazawa: from molecular structure to biological function.
  J Biochem, 148, 631-638.  
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
  18816552 E.Brustad, M.L.Bushey, J.W.Lee, D.Groff, W.Liu, and P.G.Schultz (2008).
A genetically encoded boronate-containing amino acid.
  Angew Chem Int Ed Engl, 47, 8220-8223.  
18765802 K.Oki, K.Sakamoto, T.Kobayashi, H.M.Sasaki, and S.Yokoyama (2008).
Transplantation of a tyrosine editing domain into a tyrosyl-tRNA synthetase variant enhances its specificity for a tyrosine analog.
  Proc Natl Acad Sci U S A, 105, 13298-13303.  
18784368 T.L.Hendrickson (2008).
Proofreading optimizes iodotyrosine insertion into the genetic code.
  Proc Natl Acad Sci U S A, 105, 13699-13700.  
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
17948002 T.A.Cropp, J.C.Anderson, and J.W.Chin (2007).
Reprogramming the amino-acid substrate specificity of orthogonal aminoacyl-tRNA synthetases to expand the genetic code of eukaryotic cells.
  Nat Protoc, 2, 2590-2600.  
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
16689635 L.Wang, J.Xie, and P.G.Schultz (2006).
Expanding the genetic code.
  Annu Rev Biophys Biomol Struct, 35, 225-249.  
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.