Figure 3. The mechanism of the spliced-exon-reopening (SER) reaction.

Left: structure of OiD1-5 bound to a ligated oligonucleotide in the presence of K⁺/Ca²⁺. The scissile phosphate is coordinated by the M1 and M2 ions (Ca²⁺, yellow spheres), while the reaction nucleophile (W1, cyan sphere) is coordinated by M2 and C358, similar to the 5′-exon hydrolysis reaction (Figure 1). Right: structure of OiD1-5 bound to a hydrolyzed oligonucleotide in the presence of K⁺/Mg²⁺. Upon hydrolysis, the portion of the oligonucleotide downstream of the scissile site is released, while the portion upstream of the scissile site remains bound to the intron because of its extensive base complementarity with EBS1 (not shown). In the absence of the scissile phosphate, a water molecule (W2, cyan sphere) bridges M1 and M2. See also Figure S3.