6CK5

PRPP riboswitch from T. mathranii bound to PRPP

Summary for 6CK5

• Entry DOI: 10.2210/pdb6ck5/pdb
• Descriptor: PRPP riboswitch, BARIUM ION, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: riboswitch, prpp, ykkc, rna
• Biological source: Thermoanaerobacter mathranii
• Total number of polymer chains: 2
• Total formula weight: 79227.01

Authors

Knappenberger, A.J.,Reiss, C.W.,Strobel, S.A. (deposition date: 2018-02-27, release date: 2018-06-20, Last modification date: 2023-10-04)

Primary citation

Knappenberger, A.J.,Reiss, C.W.,Strobel, S.A.
Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA.
Elife, 7:-, 2018

PubMed Abstract: Two classes of riboswitches related to the guanidine-I riboswitch bind phosphoribosyl pyrophosphate (PRPP) and guanosine tetraphosphate (ppGpp). Here we report the co-crystal structure of the PRPP aptamer and its ligand. We also report the structure of the G96A point mutant that prefers ppGpp over PRPP with a dramatic 40,000-fold switch in specificity. The ends of the aptamer form a helix that is not present in the guanidine aptamer and is involved in the expression platform. In the mutant, the base of ppGpp replaces G96 in three-dimensional space. This disrupts the S-turn, which is a primary structural feature of the RNA motif. These dramatic differences in ligand specificity are achieved with minimal mutations. aptamers are therefore a prime example of an RNA fold with a rugged fitness landscape. The ease with which the aptamer acquires new specificity represents a striking case of evolvability in RNA.

PubMed: 29877798
DOI: 10.7554/eLife.36381

Experimental method

X-RAY DIFFRACTION (2.49 Å)