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Figure 3.
Figure 3 VPg-3D polymerase interactions. (A) Structure of the
VPg primer protein (red) with the contacting residues of the 3D
polymerase shown in different colors. Four different regions of
the polymerase molecule contact VPg residues E166, I167, R168,
K172 and R179, belonging to motif F of fingers (orange),
together with residues T407, A410 and I411 of the thumb domain
(light blue), interact with the N-terminal moiety of VPg,
stabilizing the conformation of Y3 in the active site cavity. In
addition, residues E166, I167 of motif F (orange), K387 and R388
of motif E (dark blue) and T407, A410 and I411 of helix  13
(light blue) interact with the central part of the VPg protein.
Finally, the 3D residues G216, C217 and P219, located at the
beginning of helix 8
(light blue) in the fingers domain, together with the side chain
of Y336 within the C motif (yellow) of the palm domain,
establish hydrophobic contacts with R11 at the exit of the
polymerase cavity. (B) Structure of the uridylylated VPg protein
(shown in red and the linked UMP in green) with the contacting
residues of the 3D polymerase shown in blue. In addition to the
interactions described in (A), amino acids D245 of motif A
(pink) and D338 of motif C (yellow) are placed in the correct
orientation for the catalysis of the phosphodiester linkage in
the active site of the 3D protein.
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