Hammerhead Ribozyme


1. Pley, H.W., Flaherty, K.M. and McKay, D.B. (1994) Three-Dimensional Structure of a Hammerhead Ribozyme. Nature 372, 68-74. [Medline Abstract]

2. Scott, W. G., Finch, J. T. and Klug, A. (1995). The Crystal Structure of an All-RNA Hammerhead Ribozyme: A Proposed Mechanism for Catalytic Cleavage. Cell. 81, 991-1002. [Medline Abstract]


This is the crystal structure of the hammerhead ribozyme from reference 2. To color the structure as in reference 1, click here <>. The secondary structure is slightly rearranged compared to ref. 1; It is composed of two strands, but they do not correspond to substrate and ribozyme as in reference 1. Compare the secondary structure to that from reference 1, below. Note how the loop sequence has been moved to change the secondary structure. Still, the 3-D structures are remarkably similar.


To see the atoms oriented as in Fig. 3 of reference 1, click here<>. This is the region of the active site and the U-turn motif. You can show the tertiary H-bonds which help hold the U-turn in place and their distances by clicking here <>. You can also highlight the H-bonds of the regular Watson-Crick pairs in this region by clicking here < >. You can toggle off the H-bonds by reclicking the buttons.

Fig. 4 of reference 1 shows the "domain II" region of the hammerhead < >. This region of conserved residues includes two G·A base pairs, an unusual A-U pair and a standard G-C pair. To see the h-bonds of the distal half of domain II click here <>. To see the H-bonds of the proximal half, click here <>. You can also see this structure side-by-side with the first one. There is also a red/blue stereo picture of both structures available.

Nucleotide numbering help.

tRNA structure.

Hammerhead Ribozyme - Main Tutorial (Ref. 1).

Side-by-side Comparison of Hammerhead Structures.

Red/blue stereo picture of both Structures.

Back to intro to DNA-RNA structure.

Comments or Suggestions to:Jim Nolan at jnolan@tulane.edu