A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases

L‐Arginine recognition by yeast arginyl‐tRNA synthetase

“…The original subclass definition of class I aaRSs should, therefore, be revised. Our results would place ArgRS and MetRS in the same subgroup and confirm the subgroup classification proposed by Landès et al . (1995).…”

“…The first common substructure is very similar in all four enzymes; GluRS possesses an extra long loop (residues 71–80 of GluRS). This common feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995); it closes the back of the active site and may play a structural role in stabilizing the overall structure.…”

“…Neither TrpRS nor TyrRS has the second strand. This feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995). This motif is involved in the anchoring of the tRNA molecule to the synthetase platform, as seen in the crystal structure of the GlnRS–tRNA Gln complex.…”

L‐Arginine recognition by yeast arginyl‐tRNA synthetase

“…The original subclass definition of class I aaRSs should, therefore, be revised. Our results would place ArgRS and MetRS in the same subgroup and confirm the subgroup classification proposed by Landès et al . (1995).…”

“…The first common substructure is very similar in all four enzymes; GluRS possesses an extra long loop (residues 71–80 of GluRS). This common feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995); it closes the back of the active site and may play a structural role in stabilizing the overall structure.…”

“…Neither TrpRS nor TyrRS has the second strand. This feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995). This motif is involved in the anchoring of the tRNA molecule to the synthetase platform, as seen in the crystal structure of the GlnRS–tRNA Gln complex.…”

Exit Strategies for Charged tRNA from GluRS

“…Figure 4b shows that Glu41 (amino acid 3 or AA3) is conserved as either glutamate or aspartate in GluRS enzymes across all domains of life. Further, comparison of ten available crystal structures of Class I aaRSs [7, 34, 35, 36, 37, 38, 39, 40, 41, 42] reveals that in nearly all specificities a conserved aspartate or glutamate is in the same orientation in the active site and binds the α–ammonium group of the charging amino acid, confirming previous studies [11]. This residue is analogous to the “universal aspartate” found in the editing domain of LeuRS and IleRS that interacts with the same α–ammonium [43, 44].…”

Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase

“…8). Residues Tyrl25, Met129 and Asp132 from the specificity-determining helix in TrpRS correspond exactly to residues Tyr169, Gln173 and Asp176 from the corresponding helix in TyrRS, which are also highly conserved in several other class I enzymes [13]. The side chains superimpose almost exactly, except for Aspl32/AspI76, as described in more detail below.…”

L‐Arginine recognition by yeast arginyl‐tRNA synthetase

“…The original subclass definition of class I aaRSs should, therefore, be revised. Our results would place ArgRS and MetRS in the same subgroup and confirm the subgroup classification proposed by Landès et al . (1995).…”

“…The first common substructure is very similar in all four enzymes; GluRS possesses an extra long loop (residues 71–80 of GluRS). This common feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995); it closes the back of the active site and may play a structural role in stabilizing the overall structure.…”

“…Neither TrpRS nor TyrRS has the second strand. This feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995). This motif is involved in the anchoring of the tRNA molecule to the synthetase platform, as seen in the crystal structure of the GlnRS–tRNA Gln complex.…”

Exit Strategies for Charged tRNA from GluRS

“…Figure 4b shows that Glu41 (amino acid 3 or AA3) is conserved as either glutamate or aspartate in GluRS enzymes across all domains of life. Further, comparison of ten available crystal structures of Class I aaRSs [7, 34, 35, 36, 37, 38, 39, 40, 41, 42] reveals that in nearly all specificities a conserved aspartate or glutamate is in the same orientation in the active site and binds the α–ammonium group of the charging amino acid, confirming previous studies [11]. This residue is analogous to the “universal aspartate” found in the editing domain of LeuRS and IleRS that interacts with the same α–ammonium [43, 44].…”

Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase

“…8). Residues Tyrl25, Met129 and Asp132 from the specificity-determining helix in TrpRS correspond exactly to residues Tyr169, Gln173 and Asp176 from the corresponding helix in TyrRS, which are also highly conserved in several other class I enzymes [13]. The side chains superimpose almost exactly, except for Aspl32/AspI76, as described in more detail below.…”

L‐Arginine recognition by yeast arginyl‐tRNA synthetase

“…The original subclass definition of class I aaRSs should, therefore, be revised. Our results would place ArgRS and MetRS in the same subgroup and confirm the subgroup classification proposed by Landès et al . (1995).…”

“…The first common substructure is very similar in all four enzymes; GluRS possesses an extra long loop (residues 71–80 of GluRS). This common feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995); it closes the back of the active site and may play a structural role in stabilizing the overall structure.…”

“…Neither TrpRS nor TyrRS has the second strand. This feature has already been mentioned for GlnRS, GluRS and MetRS (Landès et al ., 1995). This motif is involved in the anchoring of the tRNA molecule to the synthetase platform, as seen in the crystal structure of the GlnRS–tRNA Gln complex.…”

Exit Strategies for Charged tRNA from GluRS

“…Figure 4b shows that Glu41 (amino acid 3 or AA3) is conserved as either glutamate or aspartate in GluRS enzymes across all domains of life. Further, comparison of ten available crystal structures of Class I aaRSs [7, 34, 35, 36, 37, 38, 39, 40, 41, 42] reveals that in nearly all specificities a conserved aspartate or glutamate is in the same orientation in the active site and binds the α–ammonium group of the charging amino acid, confirming previous studies [11]. This residue is analogous to the “universal aspartate” found in the editing domain of LeuRS and IleRS that interacts with the same α–ammonium [43, 44].…”

Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase

“…8). Residues Tyrl25, Met129 and Asp132 from the specificity-determining helix in TrpRS correspond exactly to residues Tyr169, Gln173 and Asp176 from the corresponding helix in TyrRS, which are also highly conserved in several other class I enzymes [13]. The side chains superimpose almost exactly, except for Aspl32/AspI76, as described in more detail below.…”