1WYD

Crystal Structure of Aspartyl-tRNA synthetase from Sulfolobus tokodaii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the nondiscriminating aspartyl-tRNA synthetase from the crenarchaeon Sulfolobus tokodaii strain 7 reveals the recognition mechanism for two different tRNA anticodons

Sato, Y.Maeda, Y.Shimizu, S.Hossain, M.T.Ubukata, S.Suzuki, K.Sekiguchi, T.Takenaka, A.

(2007) Acta Crystallogr D Biol Crystallogr 63: 1042-1047

  • DOI: 10.1107/S0907444907038292
  • Primary Citation of Related Structures:  
    1WYD

  • PubMed Abstract: 
  • In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing ...

    In protein synthesis, 20 types of aminoacyl-tRNA synthetase (aaRS) are generally required in order to distinguish between the 20 types of amino acid so that each achieves strict recognition of the cognate amino acid and the cognate tRNA. In the crenarchaeon Sulfolobus tokodaii strain 7 (St), however, asparaginyl-tRNA synthetase (AsnRS) is missing. It is believed that AspRS instead produces Asp-tRNA(Asn) in addition to Asp-tRNA(Asp). In order to reveal the recognition mechanism for the two anticodons, GUC for aspartate and GUU for asparagine, the crystal structure of St-AspRS (nondiscriminating type) has been determined at 2.3 A resolution as the first example of the nondiscriminating type of AspRS from crenarchaea. A structural comparison with structures of discriminating AspRSs indicates that the structures are similar to each other overall and that the catalytic domain is highly conserved as expected. In the N-terminal domain, however, the binding site for the third anticodon nucleotide is modified to accept two pyrimidine bases, C and U, but not purine bases. The C base can bind to form a hydrogen bond to the surrounding main-chain amide group in the discriminating AspRS, while in the nondiscriminating AspRS the corresponding amino-acid residue is replaced by proline, which has no amide H atom for hydrogen-bond formation, thus allowing the U base to be accommodated in this site. In addition, the residues that cover the base plane are missing in the nondiscriminating AspRS. These amino-acid changes make it possible for both C and U to be accepted by the nondiscriminating AspRS. It is speculated that this type of nondiscriminating AspRS has been introduced into Thermus thermophilus through horizontal gene transfer.


    Organizational Affiliation

    Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
hypothetical aspartyl-tRNA synthetaseA, B429Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Gene Names: aspSSTK_02050
EC: 6.1.1.23
Find proteins for Q976I3 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q976I3 
Go to UniProtKB:  Q976I3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download Ideal Coordinates CCD File 
E [auth A], H [auth B]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A], G [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A], F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.3α = 90
b = 139.25β = 90
c = 75.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2007-09-14
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance