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Catalytic Site Atlas

CSA LITERATURE entry for 1b7y

E.C. namephenylalanine---tRNA ligase
SpeciesThermus thermophilus (Bacteria)
E.C. Number (IntEnz)
CSA Homologues of 1b7yThere are 13 Homologs
CSA Entries With UniProtID P27001
CSA Entries With EC Number
PDBe Entry 1b7y
PDBSum Entry 1b7y
MACiE Entry 1b7y

Literature Report

IntroductionPhenylalanine 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.
MechansimThe 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.

Catalytic Sites for 1b7y

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
ArgA204204macie:sideChainStabilises the pentavalent phosphate transition state by forming favourable contacts to the alpha phosphate of ATP and the aminoacyl-AMP.
AlaA314314macie:sideChainSteric 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.

Literature References

Reshetnikova L
Crystal structures of phenylalanyl-tRNA synthetase complexed with phenylalanine and a phenylalanyl-adenylate analogue.
J Mol Biol 1999 287 555-568
PubMed: 10092459