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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1b7y
Original Entry
Title:
Ligase
Compound:
Phenylalanyl-trna synthetase
Mutant:
No
UniProt/Swiss-Prot:
P27001-SYFA_THETH
P27002-SYFB_THETH
EC Class:
6.1.1.20
Other CSA Entries:
Overview of all sites for 1b7y
Homologues of 1b7y
Entries for UniProt/Swiss-Prot: P27001
Entries for UniProt/Swiss-Prot: P27002
Entries for EC: 6.1.1.20
Other Databases:
PDB entry: 1b7y
PDBsum entry: 1b7y
UniProt/Swiss-Prot: P27001
UniProt/Swiss-Prot: P27002
IntEnz entry: 6.1.1.20
Literature Report:
Introduction:
Phenylalanine tRNA synthase is able to catalyse the addition of a phenylalanine residue to the specific tRNA needed to transfer it to the ribosome for protein synthesis. It is a member of the Class II group of amino acid tRNA synthases, which includes Histidine and Serine specific enzymes, as opposed to the Class I group including, among others, Arginine and Lysine specific enzymes. As a consequence, it shows homology with the rest of the Class II group in the residues surrounding the ATP binding site in particular, as well as some overall structural similarity. The enzyme is unusual however because it adds the amino acid to the 2' OH group of the tRNA rather than the 3'OH, the only Class II enzyme so far discovered with this functionality.
Mechanism:
The overall reaction proceeds via two steps. In the first step the amino acid is activated towards nucleophilic attack by adding an AMP moiety to the amino group; a good leaving group. This is achieved by a nucleophilic attack by the alpha amino group on the alpha phosphate of ATP, producing a pentavalent phosphate transition state which collapses to leaving the product phenylalanyl-AMP and Pyrophosphate. From this position nucleophilic attack on the amino acid's nitrogen atom by the 2'OH group of the attacking tRNA results in the formation of the final product. Each stage passes through a pentavalent phosphate transition state which is stabilised by Arg 204 and Mg2+. The discrimination of the enzyme between phenylalanine and tyrosine is achieved by Ala 314 which promotes hydrolysis of the tyrosylAMP which is formed if tyrosine reacts.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 204 204Sidechain
ElectrostaticTransition state
Stabilises the pentavalent phosphate transition state by forming favourable contacts to the alpha phosphate of ATP and the aminoacyl-AMP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10092459 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10092459 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ALAA 314 314Sidechain
Steric hindranceSubstrate
Steric hinderance from Ala 314 makes tyrosyl AMP subject to hydrolysis whilst favouring phenylalanyl AMP at the active site. This ensures the specificity of the enzyme is maintained, thus increases the overall rate at which phenylalanyl-AMP can be formed.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10092459 Current protein Mutagenesis of residue
PubMed ID 10092459 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
D1001 0
ElectrostaticTransition state
Stabilises the transition state by contacting the alpha phosphate of ATP and of the aminoacyl-AMP.
Evidence from paper Evidence concerns Evidence type
PubMed ID 10092459 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 10092459 Current protein Structural similarity to homologue of known mechanism
References:
1
Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.
L. Reshetnikova and N. Moor and O. Lavrik and D. G. Vassylyev
J Mol Biol 287, (3) 555-68, (1999).
10092459
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