3B5F

Crystal Structure of a Minimally Hinged Hairpin Ribozyme Incorporating the Ade38Dap Mutation and a 2',5' Phosphodiester Linkage at the Active Site

Summary for 3B5F

• Entry DOI: 10.2210/pdb3b5f/pdb
• Related: 2P7F 3B58 3B5A 3B5S 3B91
• Descriptor: Loop A Substrate strand, 29-mer Loop A and Loop B Ribozyme strand, Loop B S-turn strand, ... (5 entities in total)
• Functional Keywords: hairpin ribozyme; 2, 6 diaminopurine; rna; 2', 5' phosphodiester linkage, rna
• Total number of polymer chains: 3
• Total formula weight: 20144.27

Authors

MacElrevey, C.,Krucinska, J.,Wedekind, J.E. (deposition date: 2007-10-25, release date: 2008-08-12, Last modification date: 2023-08-30)

Primary citation

MacElrevey, C.,Salter, J.D.,Krucinska, J.,Wedekind, J.E.
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
Rna, 14:1600-1616, 2008

PubMed Abstract: The hairpin ribozyme requires functional groups from Ade38 to achieve efficient bond cleavage or ligation. To identify molecular features that contribute to catalysis, structures of position 38 base variants 2,6-diaminopurine (DAP), 2-aminopurine (AP), cytosine (Cyt), and guanine (Gua) were determined between 2.2 and 2.8 A resolution. For each variant, two substrate modifications were compared: (1) a 2'-O-methyl-substituent at Ade-1 was used in lieu of the nucleophile to mimic the precatalytic state, and (2) a 3'-deoxy-2',5'-phosphodiester linkage between Ade-1 and Gua+1 was used to mimic a reaction-intermediate conformation. While the global fold of each variant remained intact, the results revealed the importance of Ade38 N1 and N6 groups. Absence of N6 resulting from AP38 coincided with failure to localize the precatalytic scissile phosphate. Cyt38 severely impaired catalysis in a prior study, and its structures here indicated an anti base conformation that sequesters the imino moiety from the scissile bond. Gua38 was shown to be even more deleterious to activity. Although the precatalytic structure was nominally affected, the reaction-intermediate conformation indicated a severe electrostatic clash between the Gua38 keto oxygen and the pro-Rp oxygen of the scissile bond. Overall, position 38 modifications solved in the presence of 2'-OMe Ade-1 deviated from in-line geometry, whereas variants with a 2',5' linkage exhibited S-turn destabilization, as well as base conformational changes from syn to anti. These findings demonstrate the importance of the Ade38 Watson-Crick face in attaining a reaction-intermediate state and the sensitivity of the RNA fold to restructuring when electrostatic and shape features fail to complement.

PubMed: 18596253
DOI: 10.1261/rna.1055308

Experimental method

X-RAY DIFFRACTION (2.7 Å)