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Valyl tRNA-Synthetase ( Thermus thermophilis )

Valyl tRNA-Synthetase ( Thermus thermophilis ). Michelle Merfeld April 29, 2010 Proteins. Overall Structure. Editing Domain (“2 nd Sieve”). 862 amino acids 25 α -helices 30 β -strands. Catalytic Domain (“1 st Sieve”). C-Terminal Coiled-Coil Domain. Anticodon

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Valyl tRNA-Synthetase ( Thermus thermophilis )

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  1. Valyl tRNA-Synthetase (Thermusthermophilis) Michelle Merfeld April 29, 2010 Proteins

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

  3. 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

  4. “Double-Sieve” Concept

  5. Aminoacylation Site Interactions Hydrophobic Pocket Trp456 Trp491 Asp81 Pro42 Pro41 Asn44 Ile491

  6. KMSKS Loop Met529

  7. Editing Domain Interactions Leu269 Glu281 Glu261 Leu278 Phe264 Thr214 Tyr337

  8. Editing Hydrophilic Pocket

  9. Anticodon Binding Domain *nucleotides are in green, amino acids are in yellow

  10. Kinetics for C-term. Domain • phosphates on A20 & A21 interact through salt bridges with Arg818 and Arg843 • G19 & C56 crucial of correct positioning of 3’ CCA end of tRNA into aminoacylation catalytic site

  11. References • 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. Cell2000, 103, 793-803. • Fukai, S.; Nureki, O.; Sekine, S.; Shimada, A.; Vassylyev, D.G.; Yogoyama, S. Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase. RNA2003, 9, 100-111. • 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. • Liu, M.; Chu, W.; Liu, J.C.H.; Horowitz, J. Role of acceptor stem conformation in tRNAValrecognition by its cognate synthetase. Nucleic Acids Res.1997, 25, 4883-4890.

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