1SER

THE 2.9 ANGSTROMS CRYSTAL STRUCTURE OF T. THERMOPHILUS SERYL-TRNA SYNTHETASE COMPLEXED WITH TRNA SER


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser).

Biou, V.Yaremchuk, A.Tukalo, M.Cusack, S.

(1994) Science 263: 1404-1410

  • DOI: 10.1126/science.8128220
  • Primary Citation of Related Structures:  
    1SER

  • PubMed Abstract: 
  • The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b f ...

    The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b from the D loop into the core of the tRNA determines the orientation of the long variable arm, which is a characteristic feature of most serine specific tRNAs. On tRNA binding, the antiparallel coiled-coil domain of one subunit of the synthetase makes contacts with the variable arm and T psi C loop of the tRNA and directs the acceptor stem of the tRNA into the active site of the other subunit. Specificity depends principally on recognition of the shape of tRNA(Ser) through backbone contacts and secondarily on sequence specific interactions.


    Related Citations: 
    • Crystal Structures at 2.5 Angstroms Resolution of Seryl-tRNA Synthetase Complexed with Two Different Analogues of Seryl-Adenylate
      Belrhali, H., Yaremchuk, A.D., Tukalo, M.A., Larsen, K., Berthet-Colominas, C., Leberman, R., Beijer, B., Sproat, B., Als-Nielsen, J., Grubel, G., Legrand, J.-F., Lehmann, M., Cusack, S.
      (1994) Science 263: 1432
    • Refined Crystal Structure of the Seryl-tRNA Synthetase from Thermus Thermophilus at 2.5 Angstroms Resolution
      Fujinaga, M., Berthet-Colominas, C., Yaremchuk, A.D., Tukalo, M.A., Cusack, S.
      (1993) J Mol Biol 234: 222
    • Crystallization of the Seryl-tRNA Synthetase: TRNA(Ser) Complex of Escherichia Coli
      Price, S., Cusack, S., Borel, F., Berthet-Colominas, C., Leberman, R.
      (1993) FEBS Lett 324: 167
    • A New Crystal Form of the Complex between Seryl-tRNA Synthetase and tRNA(Ser) from Thermus Thermophilus that Diffracts to 2.8 Angstroms Resolution
      Yaremchuk, A.D., Tukalo, M.A., Krikliviy, I., Malchenko, N., Biou, V., Berthet- Colominas, C., Cusack, S.
      (1992) FEBS Lett 310: 157
    • Crystallization of the Seryl-tRNA Synthetase-tRNA(Ser) Complex from Thermus Thermophilus
      Yaremchuk, A.D., Tukalo, M.A., Krikliviy, I., Mel'nik, V.N., Berthet-Colominas, C., Cusack, S., Leberman, R.
      (1992) J Mol Biol 224: 519
    • Sequence, Structural and Evolutionary Relationships between Class 2 Aminoacyl- tRNA Synthetases
      Cusack, S., Hartlein, M., Leberman, R.
      (1991) Nucleic Acids Res 19: 3489
    • Seryl-tRNA Synthetase from Escherichia Coli at 2.5 Angstroms Resolution: A Second Class of Synthetase Structure
      Cusack, S., Berthet-Colominas, C., Hartlein, M., Nassar, N., Leberman, R.
      (1990) Nature 347: 249
    • Crystals of Seryl-tRNA Synthetase from Thermus Thermophilus. Preliminary Crystallographic Data.
      Garber, M.B., Yaremchuk, A.D., Tukalo, M.A., Egorova, S.P., Berthet-Colominas, C., Leberman, R.
      (1990) J Mol Biol 213: 631

    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, France.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))AB421Thermus thermophilusMutation(s): 0 
EC: 6.1.1.11
Find proteins for P34945 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore P34945 
Go to UniProtKB:  P34945
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
TRNASERT94Thermus thermophilus
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.5α = 90
b = 128.9β = 90
c = 121.2γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Advisory, Derived calculations