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PDBsum entry 1zh6

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protein ligands links
Ligase PDB id
1zh6
Jmol
Contents
Protein chain
307 a.a. *
Ligands
4AF
BME ×2
Waters ×80
* Residue conservation analysis
PDB id:
1zh6
Name: Ligase
Title: Crystal structure of p-acetylphenylalanine-tRNA synthetase i with p-acetylphenylalanine
Structure: Tyrosyl-tRNA synthetase. Chain: a. Synonym: tyrosine--tRNA ligase, tyrrs. Engineered: yes. Mutation: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: tyrs. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.50Å     R-factor:   0.213     R-free:   0.278
Authors: J.M.Turner,J.Graziano,G.Spraggon,P.G.Schultz
Key ref: J.M.Turner et al. (2005). Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase. J Am Chem Soc, 127, 14976-14977. PubMed id: 16248607 DOI: 10.1021/ja0549042
Date:
22-Apr-05     Release date:   04-Apr-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q57834  (SYY_METJA) -  Tyrosine--tRNA ligase
Seq:
Struc:
306 a.a.
307 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 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 = 4AF)
matches with 75.00% similarity
+ 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: 10.1021/ja0549042 J Am Chem Soc 127:14976-14977 (2005)
PubMed id: 16248607  
 
 
Structural characterization of a p-acetylphenylalanyl aminoacyl-tRNA synthetase.
J.M.Turner, J.Graziano, G.Spraggon, P.G.Schultz.
 
  ABSTRACT  
 
It has been recently shown that orthogonal tRNA/aminoacyl-tRNA synthetase pairs can be evolved to allow genetic incorporation of unnatural amino acids into proteins in both prokaryotes and eukaryotes. Here we describe the crystal structure of an evolved aminoacyl-tRNA synthetase that charges the unnatural amino acid p-acetylphenylalanine. Molecular recognition is due to altered hydrogen bonding and packing interactions with bound substrate that result from changes in both side-chain and backbone conformation.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20307192 C.C.Liu, and P.G.Schultz (2010).
Adding new chemistries to the genetic code.
  Annu Rev Biochem, 79, 413-444.  
20217843 I.T.Yonemoto, and E.M.Tippmann (2010).
The juggernauts of biology.
  Bioessays, 32, 314-321.  
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.  
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
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.  
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
17322890 W.Liu, A.Brock, S.Chen, S.Chen, and P.G.Schultz (2007).
Genetic incorporation of unnatural amino acids into proteins in mammalian cells.
  Nat Methods, 4, 239-244.  
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.  
16260173 J.Xie, and P.G.Schultz (2005).
Adding amino acids to the genetic repertoire.
  Curr Opin Chem Biol, 9, 548-554.  
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.