Extended Data Fig. 7: Stereo view of the expanded views of the ATP allosteric site of SeXPK.

a. The free state, providing the combined views of Fig.3g,i,k. b. Bound with AMPPNP, providing combined views of Fig. 3h,j,l. Comparison between the free and bound structures here and in the main text provides detailed information on the effect of ATP binding, for all 8 residues in the conserved motif P702, W703, H706, Y’710, R’711, H719, R721, R753 as well as the key helices α24 and α19. Since the main text focuses more on the interaction with α24, here we provide detailed explanation for the interaction with α24, which also involves dynamic features of W703 (density maps in Extended Data Fig. 5b). P702 resides at a turn connecting the helix α24 and the loop where W703 and Y701 respectively reside. Therefore, it provides certain degree of flexibility to the local region. In the free XPK, the W703 from one subunit can reside at two positions, swinging upwards and downwards, but alternates with the other W703. When the W703 side chain swings upwards, it partially occupies the ATP binging space. In the AMPPNP-bound structure, both W703 residues swing downwards and show subtle side chain movement (side-to-side), which is stabilized by the cation-pi interaction with K707 and an H-bond between C=O of Y701 and NH of W703. Such interaction is also likely facilitated by P702. The three residues form a beta-turn like configuration to keep W703 side chain pointing downwards and interact with D551 or N555 from helix α19. In addition, the dynamic feature of W703, assisted by its neighboring residue P702, could function as a regulatory switch in response to ATP binding.