Editing Domain (“2 nd Sieve”) Catalytic Domain (“1 st Sieve”) Anticodon Binding Domain C-Terminal Coiled-Coil Domain 862 amino acids 25 α-helices 30 β-strands.

Valyl tRNA-Synthetase(Thermus thermophilis)

Michelle MerfeldApril 29, 2010

Proteins

Editing Domain (“2nd Sieve”)

Catalytic Domain (“1st Sieve”)

Anticodon Binding Domain

C-Terminal Coiled-Coil Domain

862 amino acids 25 α-helices 30 β-strands

Overall Structure

Function

• Aminoacyl tRNA synthetases are enzymes that catalyze the esterification of a specific amino acid to a compatible cognate tRNA to form an aminoacyl-tRNA

• Class I vs. Class II:– 2’-OH, then 3’-OH– Directly to 3’-OH

“Double-Sieve” Concept

Aminoacylation Site Interactions

Hydrophobic Pocket

Pro41

Pro42

Asn44Ile491

Trp491

Trp456

Asp81

KMSKS Loop

Met529

Editing Domain Interactions

Thr214

Tyr337

Phe264

Leu269

Leu278

Glu261

Glu281

Editing Hydrophilic Pocket

Anticodon Binding Domain

*nucleotides are in green, amino acids are in yellow

Kinetics for C-term. Domaino phosphates on A20 & A21 interact through salt bridges with Arg818 and Arg843

o G19 & C56 crucial of correct positioning of 3’ CCA end of tRNA into aminoacylation catalytic site

References1. Fukai, S.; Nureki, O.; Sekine, S.; Shimada, A.; Tao, J.; Vassylyev, D.G.; Yokoyama, S.

Structural Basis for Double-Sieve Discrimination of L-Valine from L-Isoleucine and L-Threonine by the Complex of tRNAVal and Valyl-tRNA Synthetase. Cell 2000, 103, 793-803.

2. Fukai, S.; Nureki, O.; Sekine, S.; Shimada, A.; Vassylyev, D.G.; Yogoyama, S. Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase. RNA 2003, 9, 100-111.

3. Fukunaga, R.; Yokoyama, S. Structural Basis for Non-cognate Amino Acid Discrimination by the Valyl-tRNA Synthetase Editing Domain. J. Bio. Chem. 2005, 280 (33), 29937-29945.

4. Liu, M.; Chu, W.; Liu, J.C.H.; Horowitz, J. Role of acceptor stem conformation in tRNAVal

recognition by its cognate synthetase. Nucleic Acids Res. 1997, 25, 4883-4890.