PDBsum entry 2akw

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protein ligands metals Protein-protein interface(s) links
Ligase PDB id
Protein chains
266 a.a. *
785 a.a. *
Waters ×197
* Residue conservation analysis
PDB id:
Name: Ligase
Title: Crystal structure of t.Thermophilus phenylalanyl-tRNA synthe complexed with p-cl-phenylalanine
Structure: Phenylalanyl-tRNA synthetase alpha chain. Chain: a. Synonym: phenylalanine--tRNA ligase alpha chain. Phers. Phenylalanyl-tRNA synthetase beta chain. Chain: b. Synonym: phenylalanine--tRNA ligase beta chain. Phers. Ec:
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Other_details: gene phes. Other_details: gene phet
Biol. unit: Tetramer (from PDB file)
2.80Å     R-factor:   0.229     R-free:   0.234
Authors: O.M.Kotik-Kogan,N.A.Moor,D.E.Tworowski,M.G.Safro
Key ref:
O.Kotik-Kogan et al. (2005). Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase. Structure, 13, 1799-1807. PubMed id: 16338408 DOI: 10.1016/j.str.2005.08.013
04-Aug-05     Release date:   27-Dec-05    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P27001  (SYFA_THETH) -  Phenylalanine--tRNA ligase alpha subunit
350 a.a.
266 a.a.
Protein chain
Pfam   ArchSchema ?
P27002  (SYFB_THETH) -  Phenylalanine--tRNA ligase beta subunit
785 a.a.
785 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Phenylalanine--tRNA ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl- tRNA(Phe)
Bound ligand (Het Group name = 200)
matches with 92.31% similarity
+ tRNA(Phe)
+ diphosphate
+ L-phenylalanyl- tRNA(Phe)
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   5 terms 
  Biochemical function     nucleotide binding     9 terms  


DOI no: 10.1016/j.str.2005.08.013 Structure 13:1799-1807 (2005)
PubMed id: 16338408  
Structural basis for discrimination of L-phenylalanine from L-tyrosine by phenylalanyl-tRNA synthetase.
O.Kotik-Kogan, N.Moor, D.Tworowski, M.Safro.
Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of amino acids onto cognate tRNAs. Since chemical structures of various amino acids closely resemble each other, it is difficult to discriminate between them. Editing activity has been evolved by certain aaRSs to resolve the problem. In this study, we determined the crystal structures of complexes of T. thermophilus phenylalanyl-tRNA synthetase (PheRS) with L-tyrosine, p-chloro-phenylalanine, and a nonhydrolyzable tyrosyl-adenylate analog. The structures demonstrate plasticity of the synthetic site capable of binding substrates larger than phenylalanine and provide a structural basis for the proofreading mechanism. The editing site is localized at the B3/B4 interface, 35 A from the synthetic site. Glubeta334 plays a crucial role in the specific recognition of the Tyr moiety in the editing site. The tyrosyl-adenylate analog binds exclusively in the synthetic site. Both structural data and tyrosine-dependent ATP hydrolysis enhanced by tRNA(Phe) provide evidence for a preferential posttransfer editing pathway in the phenylalanine-specific system.
  Selected figure(s)  
Figure 3.
Figure 3. View of the Editing Site of T. thermophilus PheRS Showing the Interactions with L-Tyrosine
(A) PheRS editing site (colored green) with bound Tyr (colored orange). The electron density map is contoured at 2.5s. The protein residues participating in direct and water-mediated (red spheres) contacts are shown.
(B) Schematic drawing of the interactions with Tyr. Direct and water (marked as S)-mediated H bonds are shown by dashed lines. Van der Waals interactions are depicted by solid arrows.
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1799-1807) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21082706 I.Mermershtain, I.Finarov, L.Klipcan, N.Kessler, H.Rozenberg, and M.G.Safro (2011).
Idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of E. coli phenylalanyl-tRNA synthetase complexed with phenylalanine and AMP.
  Protein Sci, 20, 160-167.
PDB code: 3pco
20223217 I.Finarov, N.Moor, N.Kessler, L.Klipcan, and M.G.Safro (2010).
Structure of human cytosolic phenylalanyl-tRNA synthetase: evidence for kingdom-specific design of the active sites and tRNA binding patterns.
  Structure, 18, 343-353.
PDB code: 3l4g
20235827 O.Khersonsky, and D.S.Tawfik (2010).
Enzyme promiscuity: a mechanistic and evolutionary perspective.
  Annu Rev Biochem, 79, 471-505.  
19189362 B.R.Villiers, and F.Hollfelder (2009).
Mapping the limits of substrate specificity of the adenylation domain of TycA.
  Chembiochem, 10, 671-682.  
19285947 J.Ling, B.R.So, S.S.Yadavalli, H.Roy, S.Shoji, K.Fredrick, K.Musier-Forsyth, and M.Ibba (2009).
Resampling and editing of mischarged tRNA prior to translation elongation.
  Mol Cell, 33, 654-660.  
19379069 J.Ling, N.Reynolds, and M.Ibba (2009).
Aminoacyl-tRNA synthesis and translational quality control.
  Annu Rev Microbiol, 63, 61-78.  
18611382 L.Klipcan, I.Levin, N.Kessler, N.Moor, I.Finarov, and M.Safro (2008).
The tRNA-induced conformational activation of human mitochondrial phenylalanyl-tRNA synthetase.
  Structure, 16, 1095-1104.
PDB code: 3cmq
17095543 B.Zhu, M.W.Zhao, G.Eriani, and E.D.Wang (2007).
A present-day aminoacyl-tRNA synthetase with ancestral editing properties.
  RNA, 13, 15-21.  
  17768348 I.Levin, N.Kessler, N.Moor, L.Klipcan, E.Koc, P.Templeton, L.Spremulli, and M.Safro (2007).
Purification, crystallization and preliminary X-ray characterization of a human mitochondrial phenylalanyl-tRNA synthetase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 761-764.  
17027500 T.Crepin, A.Yaremchuk, M.Tukalo, and S.Cusack (2006).
Structures of two bacterial prolyl-tRNA synthetases with and without a cis-editing domain.
  Structure, 14, 1511-1525.
PDB codes: 2i4l 2i4m 2i4n 2i4o 2j3l 2j3m
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.