Protein Name

RNA hammerhead ribozyme


Mus musculus (house mouse)

Biological Context

One small atom can make a big difference. What most prominently separates deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), is an extra hydroxyl group (OH) attached to the sugar that is part of the molecular backbone. The result however is amazing difference in structural diversity. While DNA mainly comes along as double-stranded helices, RNA can take on many shapes and functions. Transfer RNA (tRNA) with its L-shaped structure is a prominent example. Until not long ago the only biochemical substances known to catalyze chemical reactions were proteins, the enzymes. It came as quite a surprise when it was discovered that RNA can also catalyze chemical reactions and act like an enzyme. Thomas Cech and Sydney Altman were awarded the 1989 Nobel prize in chemistry for discovering the catalytic properties of RNA. Such RNA is called a ribozyme, in analogy to enzyme. Since the production of proteins from DNA, in addition to RNA, requires proteins, there has always been the question about the hen and the egg. How did life develop? To generate proteins from DNA, proteins are already needed. Where do they come from? Therefore, after the discovery of ribozymes, it has been proposed that life started with RNA and that all other life evolved from there. This question is still unanswered.

Structure Description


The ribozyme shown here is aptly called a hammerhead ribozyme because it is shaped like the two heads of a hammer. Compared to the double strands of a DNA helix or even to the more elaborate shape of a tRNA molecule, it has an amazingly intricate shape. Even though the molecule consists of four separate chains of RNA, they form such a complicated pattern of base- pair matching that it is hard to tell where the chains start and where they end. And what is less obvious: the A and C chains are shorter than the B and D chains. The A and C chains form base-pairs with residues from the B and D chains, but the B and D chains have an extra twist a the top of the head where they form base-pairs with themselves. Essentially the molecule is a dimer consisting of two monomers, A/B and C/D. From the structure conclusions are drawn, how with the help of magnesium ions, also present, the ribozyme can cleave itself.

Protein Data Bank (PDB)



Scott, W.G. Finch, J.T. Klug, A.; "The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage."; Cell; (1995) 81:991-1002 PubMed:7541315.


author: Arno Paehler

Japanese version:PDB:1MME