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: 2.9 Å
  • R-Value Work: 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


  • 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: 
    • 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
    • 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
    • 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
    • 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
    • Sequence, Structural and Evolutionary Relationships between Class 2 Aminoacyl- tRNA Synthetases
      Cusack, S.,Hartlein, M.,Leberman, R.
      (1991) Nucleic Acids Res. 19: 3489
    • 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
    • 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
    • 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


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble Outstation, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11))
A, B
421Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: serS
EC: 6.1.1.11
Find proteins for P34945 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P34945
Entity ID: 1
MoleculeChainsLengthOrganism
TRNASERT94Thermus thermophilus
Small Molecules
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
T
RNA LINKINGC9 H13 N2 O9 PU
5MU
Query on 5MU
T
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
T
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 124.500α = 90.00
b = 128.900β = 90.00
c = 121.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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