Hammerhead Ribozyme

References:

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]

I. Ribozyme and Substrate

The minimal consensus structure for the hammerhead ribozyme is shown above. The sequences shown as outlines are required for efficient cleavage. Residues indicated by N can be any base and N´ indicates the complement of the base with which it is paired. The H at the cleavage site means any base but G. The lines at the ends of stems I, II , and III indicate that any number of bases may connect the two halves of each stem, or they need not be connected at all. In the 3-D structure to the left and the secondary structure above, the strand cleaved is shown in red and the rest of the molecule is shown in blue.

II. Tertiary structure

In the secondary structure below, the hammerhead is colored as it is in reference 1. Click here < > to color the 3-D structure like the secondary structure below. Substrate is the green strand and much of the ribozyme is magenta. The "U-turn" motif near the active site of the ribozyme strand, which holds the RNA in the proper conformation for cleavage, is highlighted. The authors refer to the U-turn as domain I. The conserved bases that form half of domain II are shown in cyan. The bond cleaved is shown as a thick bond. For cleavage to occur, the residue 5´ to the cleavage site must have a 2´-OH. To prevent cleavage during the crystallization process, the substrate strand was constructed entirely of DNA, rather than RNA in reference 1; thus the 2-OH necessary for cleavage was missing. In reference 2, the substrate was composed of RNA, but the residue 5´ to the cleavage site had a methyl group added to the 2´-OH to prevent cleavage.

An alternative representation can be seen using this button <>. The backbone is represented by a colored ribbon. The conserved bases of domains I and II are shown as wireframes. Also shown, as yellow spheres, are phosphate oxygens which are believed to be sites of coordination of Mg++ ions. When these sites are substituted by S, cleavage is inhibited, due to reduced Mg++ binding at these important sites. Looking at this end view of the structure &lt >, you can see that stems II and III form a nearly continuous helix, while the U-turn holds stem I out to the side.

This representation <> also illustrates the point. The view is from the normal angle, but the bases are shown as space-filling models. See how the stemII-domainII-stemIII region forms a continuous stacked helix.

IIa. U-turn

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 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. For more information on U-turns, see the tRNA structure tutorial or the stereo picture of tRNA U-turns.

IIb. Domain II

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 <>. There is also a short tutorial on a second hammerhead ribozyme crystal structure available. You can also see the two 3D structures side-by-side or a red/blue stereo picture of both structures.


Nucleotide numbering help.

tRNA structure.

Hammerhead Ribozyme - (Ref. 2).

Side-by-side Comparison of Hammerhead Structures.

Red/blue stereo picture of both Structures.

Back to intro to DNA-RNA structure.