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PDBsum entry 1u7d

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protein Protein-protein interface(s) links
Ligase PDB id
1u7d
Jmol
Contents
Protein chains
292 a.a. *
Waters ×37
* Residue conservation analysis
PDB id:
1u7d
Name: Ligase
Title: Crystal structure of apo m. Jannashii tyrosyl-tRNA synthetase
Structure: Tyrosyl-tRNA synthetase. Chain: a, b. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: tyrs. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.65Å     R-factor:   0.227     R-free:   0.277
Authors: Y.Zhang,L.Wang,P.G.Schultz,I.A.Wilson
Key ref:
Y.Zhang et al. (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. PubMed id: 15840835 DOI: 10.1110/ps.041239305
Date:
03-Aug-04     Release date:   17-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q57834  (SYY_METJA) -  Tyrosine--tRNA ligase
Seq:
Struc:
306 a.a.
292 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
+ 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: 10.1110/ps.041239305 Protein Sci 14:1340-1349 (2005)
PubMed id: 15840835  
 
 
Crystal structures of apo wild-type M. jannaschii tyrosyl-tRNA synthetase (TyrRS) and an engineered TyrRS specific for O-methyl-L-tyrosine.
Y.Zhang, L.Wang, P.G.Schultz, I.A.Wilson.
 
  ABSTRACT  
 
The Methanococcus jannaschii tRNA(Tyr)/TyrRS pair has been engineered to incorporate unnatural amino acids into proteins in E. coli. To reveal the structural basis for the altered specificity of mutant TyrRS for O-methyl-L-tyrosine (OMeTyr), the crystal structures for the apo wild-type and mutant M. jannaschii TyrRS were determined at 2.66 and 3.0 A, respectively, for comparison with the published structure of TyrRS complexed with tRNA(Tyr) and substrate tyrosine. A large conformational change was found for the anticodon recognition loop 257-263 of wild-type TyrRS upon tRNA binding in order to facilitate recognition of G34 of the anticodon loop through pi-stacking and hydrogen bonding interactions. Loop 133-143, which is close to the tRNA acceptor stem-binding site, also appears to be stabilized by interaction with the tRNA(Tyr). Binding of the substrate tyrosine results in subtle and cooperative movements of the side chains within the tyrosine-binding pocket. In the OMeTyr-specific mutant synthetase structure, the signature motif KMSKS loop and acceptor stem-binding loop 133-143 were surprisingly ordered in the absence of bound ATP and tRNA. The active-site mutations result in altered hydrogen bonding and steric interactions which favor binding of OMeTyr over L-tyrosine. The structure of the mutant and wild-type TyrRS now provide a basis for generating new active-site libraries to evolve synthetases specific for other unnatural amino acids.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Comparison of wild-type apo and bound M. jannaschii TyrRS's. (A) Stereo view of the B-value distribution of the apo wild-type M. jannaschii TyrRS structure. The structure trace is colored by B-values with a gradient ranging from low (25 2, blue) through medium (average B-value 59 2, yellow) to high (100 2, red), which highlights the more disordered regions of the structure (red). (B) Stereo view of the superimposition of apo wild-type M. jannaschii TyrRS and the bound structure (PDB code 1j1u [PDB] ;Kobayashi et al. 2003) of M. jannaschii TyrRS with tRNA (blue). Complexed M. jannaschii TyrRS is colored by its rms deviation (C ) from the apo wild-type TyrRS structure (gray) with a gradient ranging from low (0.2 , green) via medium (1.8 , yellow) to high (>4.0 , red).
Figure 5.
Figure 5. Amino acid-binding site in wild-type TyrRS and OMeTyr-specific mutant. (A) Hydrophobic interactions and hydrogen bonds between substrate tyrosine and M. jannaschii TyrRS. Hydrogen bonds are represented with dashed lines and labeled with distances in , and hydrophobic interactions are indicated by red spiked arcs. The distances in parentheses in red are the distances between the apo enzyme superimposed on the tyrosine ligand position from the bound structure (Kobayashi et al. 2003). (B) Stereo view of the superimposition of wild-type M. jannaschii TyrRS and OMeTyr-specific mutant synthetase to illustrate conformational differences. Apo mutant M. jannaschii TyrRS is colored by its rms deviation (C ) from the apo wild-type TyrRS structure (gray) with a gradient ranging from low (0.2 , green) via medium (1.8 , yellow) to high (>4.0 , red). (C) Stereo view of OMeTyr-specific mutant synthetase superimposed with wild-type apo M. jannaschii TyrRS (gray) to highlight mutated residues. The mutant enzyme is colored with cyan helices and pink -strands. The four residues subjected to mutation are represented by ball-and-stick with their oxygen atoms colored red. Bonds/carbon atoms are colored green in the mutant enzyme but blue in wild-type.
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 1340-1349) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
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
18596202 M.Chen, L.Cai, Z.Fang, H.Tian, X.Gao, and W.Yao (2008).
Site-specific incorporation of unnatural amino acids into urate oxidase in Escherichia coli.
  Protein Sci, 17, 1827-1833.  
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.  
17878972 D.J.Maloney, N.Ghanem, J.Zhou, and S.M.Hecht (2007).
Positional assignment of differentially substituted bisaminoacylated pdCpAs.
  Org Biomol Chem, 5, 3135-3138.  
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
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.  
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.