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The vibronic peak at 519 nm and shoulder at 563 nm in the PSDT-C12 film further confirmed stronger main chain interaction.
PSDT-C12 has a longer main chain (larger molecule weight) than PSDT-EH, which can favour a more extended main chain interaction.
However, the peptide main chain interaction with the SH3 domains is conserved.
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Thr-250 binds γ-phosphate through main chain interactions and Thr-251 (corresponding to Thr-35 in Ras) coordinates the γ-phosphate and also the Mg2+.
Briefly, main chain interactions between the backbone carbonyl and amide groups of Leu17 and Leu20, respectively, allow hydrogen-bond formation with the C2 amine of residue G0.
The K-loop also harbors a conserved motif 249GTTRD253 in switch-I region (Thr-251 corresponds to Thr-35 in Ras that coordinates both Mg2+ and γ-phosphate) and coordinates the K+ ion through main chain interactions via Thr-245 and Ile-247 [23].
While it seems that active site dimension contributes to potassium specificity, inspection of the active site of YqeH model suggests that like in MnmE, potassium is bound at the active site by main chain interactions with a part of switch-I, termed the K-loop, α and β phosphates of GDP, a fluoride ion (i.e. the γ-phosphate mimic) and the side chain of Asn-169 from P-loop (Fig. 4a).
Additional hydrogen bonds stabilize the peptide-motor complex through main chain interactions.
Consequently, tight binding of Tah1 to Hsp90 is determined within the conserved MEEVD motif, and upstream amino acids appear to be involved in mainly main chain interactions.
These data indicate that main chain interactions are critical for substrate binding, and the lack of a β-turn in the peptide substrate indicates that PRMT7 may accommodate a wider range of peptide sequences apart from glycine-rich elements.
The side chain amide of Asn is also involved in main chain interactions with the backbone amide of the terminal aspartate residue, whereas the guanidinium group of Arg also contacts the main chain carbonyl and amide (via a water molecule) of Glu−2 (S−6RMEEVD).
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