Structure of pyrrolysyl-tRNA synthetase, an archaeal enzyme for genetic code innovation.
Pyrrolysine (Pyl), the 22nd natural amino acid and genetically encoded by UAG, becomes attached to its cognate tRNA by pyrrolysyl-tRNA synthetase (PylRS). We have determined three crystal structures of the Methanosarcina mazei PylRS complexed with either AMP-PNP, Pyl-AMP plus pyrophosphate, or the Pyl analogue N-epsilon-[(cylopentyloxy)carbonyl]-L-lysine plus ATP. The structures reveal that PylRS utilizes a deep hydrophobic pocket for recognition of the Pyl side chain. A comparison of these structures with previously determined class II tRNA synthetase complexes illustrates that different substrate specificities derive from changes in a small number of residues that form the substrate side-chain-binding pocket. The knowledge of these structures allowed the placement of PylRS in the aminoacyl-tRNA synthetase (aaRS) tree as the last known synthetase that evolved for genetic code expansion, as well as the finding that Pyl arose before the last universal common ancestral state. The PylRS structure provides an excellent framework for designing new aaRSs with altered amino acid specificity.
Kavran
Jennifer M
JM
Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, CT 06520-8114, USA.
Gundllapalli
Sarath
S
O'Donoghue
Patrick
P
Englert
Markus
M
Söll
Dieter
D
Steitz
Thomas A
TA
D000604:Amino Acyl-tRNA Synthetases / Q000737:chemistry* / Q000145:classification / Q000235:genetics*; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics*; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D005815:Genetic Code; D057927:Hydrophobic and Hydrophilic Interactions; D008239:Lysine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D017020:Methanosarcina / Q000201:enzymology* / Q000235:genetics*; D013379:Substrate Specificity
D019843:Archaeal Proteins; D000604:Amino Acyl-tRNA Synthetases; C456839:pyrrolysine; D008239:Lysine