Extended Data Fig. 7: Comparison of guanine binding in the MTR1 ribozyme compared with guanine-related ligand binding in some riboswitch structures.
From: Structure and mechanism of a methyltransferase ribozyme
Comparison of guanine binding in the MTR1 ribozyme compared with guanine-related ligand binding in some riboswitch structures. The orientation of the ligand (highlighted in cyan) is similar in all the images. a. MTR1 ribozyme (this work). b. The guanine riboswitch. PDB ID 6UBU2. The binding of the guanine ligand by cytosine and uracil nucleobases is closely similar to that found in MTR1. c. The PreQ1-I riboswitch. PDB ID 3Q503. The Watson-Crick edge of the pre-queuosine1 (preQ1) ligand is bound by cytosine, while the sugar edge is bound by the Watson-Crick edge of an adenine at N1 and N6, and makes a single hydrogen bond with a uracil O4. d. The PreQ1-II riboswitch. PDB ID 4JF24. The sugar edge of the preQ1 ligand is bound by a uracil in a similar manner to MTR1, except that the roles of U O2 and O4 are reversed. The Watson-Crick edge is bound by O2 and N3 of a cytosine. e and f. The cyclic-di-GMP riboswitch. PDB ID 3IRW5. The ligand comprises two guanine nucleobases, bound in different environments. The Watson-Crick edge of the guanine shown in part e is once again bound to cytosine, while the sugar edge is bound to N1 and N6 of an adenine. By contrast the other guanine (part f) is only bound on its Hoogsteen edge, making two hydrogen bonds to the Watson-Crick edge of a guanine at N1 and N2.
