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. Author manuscript; available in PMC: 2016 Jan 30.
Published in final edited form as: Nature. 2015 Jun 29;523(7562):621–625. doi: 10.1038/nature14482

Figure 2.

Figure 2

Interaction between 5caC and epi-DNA recognition loop compromises GTP incorporation. a, The Pol II EC structure containing a matched GMPCPP opposite 5caC site (EC-II). The color codes are the same as Fig. 1 except for 5caC (yellow) and GMPCPP (orange). b–d, The GMPCPP:5caC base pair is shifted toward the downstream main channel from the canonical GMPCPP:dC position (PDB: 2E2J). The side chain of Rpb2 Q531 rotates 100 degrees to interact with 5caC (b and c). e–g, Comparison of catalytic rate constants (kpol) (e), substrate dissociation constants Kd,app (f), and specificity constants (kpol/Kd,app) (g) of GTP incorporation opposite 5caC template by wt, Q531H, and Q531A Pol II, respectively. The mean values are presented and error bars are standard deviations derived from three independent experiments.