1FYF

CRYSTAL STRUCTURE OF A TRUNCATED FORM OF THREONYL-TRNA SYNTHETASE COMPLEXED WITH A SERYL ADENYLATE ANALOG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem.

Dock-Bregeon, A.Sankaranarayanan, R.Romby, P.Caillet, J.Springer, M.Rees, B.Francklyn, C.S.Ehresmann, C.Moras, D.

(2000) Cell 103: 877-884

  • DOI: 10.1016/s0092-8674(00)00191-4
  • Primary Citation of Related Structures:  
    1FYF

  • PubMed Abstract: 
  • Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step ...

    Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.


    Related Citations: 
    • The Structure of Threonyl-tRNA Synthetase-tRNA(Thr) Complex Enlightens its Repressor Activity and Reveals an Essential Zinc Ion in the Active Site
      Sankaranarayanan, R., Dock-Bregeon, A.C., Romby, P., Caillet, J., Springer, M., Rees, B., Ehresmann, C., Ehresmann, B., Moras, D.
      (1999) Cell 97: 371
    • Zinc Ion Mediated Amino Acid Discrimination by Threonyl-tRNA Synthetase
      Sankaranarayanan, R., Dock-Bregeon, A.C., Rees, B., Bovee, M., Caillet, J., Romby, P., Francklyn, C.S., Moras, D.
      (2000) Nat Struct Biol 7: 461

    Organizational Affiliation

    UPR 9004 Biologie Structurale IGBMC, CNRS/INSERM/ULP BP163 67404 Cedex, Illkirch, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THREONYL-TRNA SYNTHETASEA, B401Escherichia coliMutation(s): 0 
EC: 6.1.1.3
UniProt
Find proteins for P0A8M3 (Escherichia coli (strain K12))
Explore P0A8M3 
Go to UniProtKB:  P0A8M3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8M3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSA
Query on SSA

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.95α = 90
b = 109.52β = 90
c = 115.37γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-12-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance