1SES

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: 2.50 Å
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 

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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

  • DOI: 10.1126/science.8128224
  • Primary Citation of Related Structures:  
    1SES, 1SET

  • 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 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 ...

    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: 
    • 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
    • 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: 

    EMBL Grenoble Outstation, France.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERYL-tRNA SYNTHETASEA, B421Thermus thermophilusMutation(s): 0 
EC: 6.1.1.11
UniProt
Find proteins for P34945 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore P34945 
Go to UniProtKB:  P34945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34945
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AHX
Query on AHX
Download Ideal Coordinates CCD File 
C [auth A]SERYL-HYDROXAMATE-ADENOSINE MONOPHOSPHATE
C13 H20 N7 O9 P
WBBUFKBXWUDMQG-YTMOPEAISA-N		 Ligand Interaction
AMP
Query on AMP
Download Ideal Coordinates CCD File 
D [auth B]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.176 
  • R-Value Observed: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.1α = 90
b = 125.2β = 108.8
c = 62.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

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