1SET

CRYSTAL STRUCTURES AT 2.5 ANGSTROMS RESOLUTION OF SERYL-TRNA SYNTHETASE COMPLEXED WITH TWO DIFFERENT ANALOGUES OF SERYL-ADENYLATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate.

Belrhali, H.Yaremchuk, A.Tukalo, M.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: 1432-1436

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monop ...

    Crystal structures of seryl-tRNA synthetase from Thermus thermophilus complexed with two different analogs of seryl adenylate have been determined at 2.5 A resolution. The first complex is between the enzyme and seryl-hydroxamate-AMP (adenosine monophosphate), produced enzymatically in the crystal from adenosine triphosphate (ATP) and serine hydroxamate, and the second is with a synthetic analog of seryl adenylate (5'-O-[N-(L-seryl)-sulfamoyl]adenosine), which is a strong inhibitor of the enzyme. Both molecules are bound in a similar fashion by a network of hydrogen bond interactions in a deep hydrophilic cleft formed by the antiparallel beta sheet and surrounding loops of the synthetase catalytic domain. Four regions in the primary sequence are involved in the interactions, including the motif 2 and 3 regions of class 2 synthetases. Apart from the specific recognition of the serine side chain, the interactions are likely to be similar in all class 2 synthetases.


    Related Citations: 
    • 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
    • Sequence, Structural and Evolutionary Relationships between Class 2 Aminoacyl-tRNA Synthetases
      Cusack, S.,Hartlein, M.,Leberman, R.
      (1991) Nucleic Acids Res. 19: 3489
    • The 2.9 Angstroms Crystal Structure of T. Thermophilus Seryl-tRNA Synthetase Complexed with tRNA-Ser
      Biou, V.,Yaremchuk, A.,Tukalo, M.,Cusack, S.
      (1994) Science 263: 1404
    • 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
    • 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
    • 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
    • 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


    Organizational Affiliation

    EMBL Grenoble Outstation, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERYL-tRNA SYNTHETASE
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SSA
Query on SSA

Download SDF File 
Download CCD File 
A, B
5'-O-(N-(L-SERYL)-SULFAMOYL)ADENOSINE
C13 H19 N7 O8 S
HQXFJGONGJPTLZ-YTMOPEAISA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 86.400α = 90.00
b = 126.300β = 109.00
c = 62.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-02-29
    Type: Database references