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. Author manuscript; available in PMC: 2016 Oct 6.
Published in final edited form as: Biochemistry. 2015 Oct 6;54(39):6114–6122. doi: 10.1021/acs.biochem.5b00406

Figure 4.

Figure 4

Linkages that stabilize cap closure and the positive-synergy conformation of the lower lip. This structure, which is of the E·PAPS· 2-Nap complex, was predicted using GROMACS. 2-Nap is a positive-synergy acceptor, and the enzyme has assumed the same positive-synergy conformation seen in Figure 1. The R group interactions labeled 1–3 appear to stabilize the closed state of the cap; they are broken as the cap opens. All of the linkages are located in the acceptor-half active-site cap. The cap is colored light blue, and the lower lip is colored red. Each linkage was disrupted via mutagenesis, and the mutants were tested for cap opening, nucleotide binding, and positive synergy.