Hairpin Ribozyme (undocked form)

S.E. Butcher, F.H.-T. Allain, and J. Feigon: "Solution structure of the Loop B domain from the hairpin ribozyme", Nature Struct. Biol. 6, 212-216 (1999). [abstract]

PDB Code: 1B36

Model of the hairpin ribozyme in its undocked form based on the present structure of the catalytic loop B domain and the structure of the substrate-binding domain loop A. The substrate strand is green. The ribozyme is shown just prior to the docking step, to illustrate the relationship between the two domains. The cleavage-site 2'-OH is indicated with a pink sphere. Atoms implicated in domain docking from chemical-probing and substitution studies are shown as red, orange and cyan spheres. Red spheres are 2'-OH, which are catalytically important. Orange and cyan spheres indicate sites of DMS reactivity at AN1 and CN3 and reactivity to Fe(II)EDTA at C4', respectively, in the undocked ribozyme that become protected upon docking. These sites show that docking involves extensive interactions between the minor-groove faces of the internal loop A and loop B. The model of the entire hairpin ribozyme was generated from the loop A coordinates and the loop B coordinates (this work). Missing nucleotides at the 3' and 5' ends of loop A and the interface between the loops were modeled from fiber diffraction A-RNA coordinates using Insight II (MSI/Biosym). Each end of these fragments contained one nucleotide already present in the given coordinate files of loop A and loop B. The fragments and loop structures were linked using r.m.s.d. superpositions of the duplicated nucleotides to yield a combined coordinate set. This raw model was then refined with 1,000 steps of rigid-body energy minimization in X-PLOR to relieve remaining steric clash.