Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 96554.20 
• Atom Count: 6799 
• Residue Count: 842 
• Unique protein chains: 1

1SES

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

• DOI: 10.2210/pdb1SES/pdb

• Classification: LIGASE
• Organism(s): Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)


• Deposited: 1994-02-21 Released: 1994-07-31 
• Deposition Author(s): Cusack, S., Belrhali, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Work: 0.176 

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

• PubMed: 8128224 
• Primary Citation of Related Structures:  
  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. 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.

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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
• 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
• 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
• 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




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Organizational Affiliation: 

EMBL Grenoble Outstation, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SERYL-tRNA SYNTHETASE	A, B	421	Thermus 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
AHX	A	SERYL-HYDROXAMATE-ADENOSINE MONOPHOSPHATE C13 H20 N7 O9 P WBBUFKBXWUDMQG-YTMOPEAISA-N
AMP	B	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Work: 0.176 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 85.100	α = 90.00
b = 125.200	β = 108.80
c = 62.400	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1994-02-21 
• Released Date: 1994-07-31 
• Deposition Author(s): Cusack, S., Belrhali, H.

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