3A32

Crystal structure of putative threonyl-tRNA synthetase ThrRS-1 from Aeropyrum pernix


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

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This is version 1.2 of the entry. See complete history


Literature

Two complementary enzymes for threonylation of tRNA in crenarchaeota: crystal structure of Aeropyrum pernix threonyl-tRNA synthetase lacking a cis-editing domain

Shimizu, S.Juan, E.C.M.Sato, Y.Miyashita, Y.Hoque, M.M.Suzuki, K.Sagara, T.Tsunoda, M.Sekiguchi, T.Dock-Bregeon, A.-C.Moras, D.Takenaka, A.

(2009) J Mol Biol 394: 286-296

  • DOI: 10.1016/j.jmb.2009.09.018
  • Primary Citation of Related Structures:  
    3A31, 3A32

  • PubMed Abstract: 
  • In protein synthesis, threonyl-tRNA synthetase (ThrRS) must recognize threonine (Thr) from the 20 kinds of amino acids and the cognate tRNA(Thr) from different tRNAs in order to generate Thr-tRNA(Thr). In general, an organism possesses one kind of gene corresponding to ThrRS ...

    In protein synthesis, threonyl-tRNA synthetase (ThrRS) must recognize threonine (Thr) from the 20 kinds of amino acids and the cognate tRNA(Thr) from different tRNAs in order to generate Thr-tRNA(Thr). In general, an organism possesses one kind of gene corresponding to ThrRS. However, it has been recently found that some organisms have two different genes for ThrRS in the genome, suggesting that their proteins ThrRS-1 and ThrRS-2 function separately and complement each other in the threonylation of tRNA(Thr), one for catalysis and the other for trans-editing of misacylated Ser-tRNA(Thr). In order to clarify their three-dimensional structures, we performed X-ray analyses of two putatively assigned ThrRSs from Aeropyrum pernix (ApThrRS-1 and ApThrRS-2). These proteins were overexpressed in Escherichia coli, purified, and crystallized. The crystal structure of ApThrRS-1 has been successfully determined at 2.3 A resolution. ApThrRS-1 is a dimeric enzyme composed of two identical subunits, each containing two domains for the catalytic reaction and for anticodon binding. The essential editing domain is completely missing as expected. These structural features reveal that ThrRS-1 catalyzes only the aminoacylation of the cognate tRNA, suggesting the necessity of the second enzyme ThrRS-2 for trans-editing. Since the N-terminal sequence of ApThrRS-2 is similar to the sequence of the editing domain of ThrRS from Pyrococcus abyssi, ApThrRS-2 has been expected to catalyze deaminoacylation of a misacylated serine moiety at the CCA terminus.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable threonyl-tRNA synthetase 1A471Aeropyrum pernixMutation(s): 0 
Gene Names: APE0809.1
EC: 6.1.1.3
Find proteins for Q9YDW0 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YDW0 
Go to UniProtKB:  Q9YDW0
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.486α = 90
b = 103.71β = 90
c = 112.537γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-11-20
    Changes: Database references