3CR1: Crystal Structure Of A Minimal, Mutant, All-Rna Hairpin Ribozyme (A38c, A-1oma) Grown From Mgcl2

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.
PDB ID: 3CR1Download
MMDB ID: 66308
PDB Deposition Date: 2008/4/4
Updated in MMDB: 2008/09
Experimental Method:
x-ray diffraction
Resolution: 2.25  Å
Source Organism:
Biological Unit for 3CR1: trimeric; determined by author and by software (PISA)
Molecular Components in 3CR1
Label Count Molecule
Nucleotides(3 molecules)
RNA (5'-r(*up*cp*cp*cp*(a2m)p*gp*up*cp*cp*ap*cp*cp*g)-3')
Molecule annotation
Loop a and B Ribozyme Strand
Molecule annotation
RNA (5'- R(*up*cp*gp*up*gp*gp*up*cp*cp*ap*up*up*ap*cp*cp*up*gp*cp*c)-3')
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB