PT  - JOURNAL ARTICLE
AU  - Daria N. Shalaeva
AU  - Dmitry A. Cherepanov
AU  - Michael Y. Galperin
AU  - Armen Y. Mulkidjanian
TI  - Comparative analysis of active sites in P-loop nucleoside triphosphatases suggests an ancestral activation mechanism
AID  - 10.1101/439992
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 439992
4099  - http://biorxiv.org/content/early/2018/10/11/439992.short
4100  - http://biorxiv.org/content/early/2018/10/11/439992.full
AB  - P-loop nucleoside triphosphatases (NTPases) share common Walker A (P-loop) and Walker B sequence motifs and depend on activating moieties (Arg or Lys fingers or a K+ ion). In search for a common catalytic mechanism, we combined structure comparisons of active sites in major classes of P-loop NTPases with molecular dynamics (MD) simulations of the Ras GTPase, a well-studied oncoprotein. Comparative structure analysis showed that positively charged activating moieties interact with gamma-phosphate groups of NTP substrates in all major classes of P-loop NTPases. In MD simulations, interaction of the activating Arg finger with the Mg-GTP-Ras complex led to the rotation of the gamma-phosphate group by 40 degrees enabling its interaction with the backbone amide group of Gly13. In all analyzed structures, the residue that corresponds to Gly13 of Ras was in a position to stabilize gamma-phosphate after its rotation, suggesting a common ancestral activation mechanism within the entire superfamily.