Archaeoglobus fulgidus (Archaea)
Transfer RNAs (tRNAs), a kind of single stranded RNAs, have an important role in transporting amino acids to ribosome during the protein synthetic process. Although most of 70-90 bases which constitute tRNA are synthesized by RNA polymerase based on DNA templates, the 3'-terminal CCA sequence (cytidine-cytidine-adenosine) which is the amino acid combining site is synthesized by the CCA-adding enzyme.(Refer to Fig.1).
The CCA-adding enzyme belongs to nucleotidyltransferase (NT) family. It adds the base sequence using ATP and CPT as materials. The most remarkable feature of this enzyme is that it can add the defined base sequence (CCA) to tRNA without any DNA/RNA templates. This enzyme is conserved among all known species. It is divided into two classes. The CCA-adding enzymes from archaea belong to class I, and the CCA-adding enzymes from eubacteria and eukaryote to class II. There is very little amino acid sequence similarity between the two classes.
The structure shown here is the class I CCA-adding enzyme from a hyperthermophilic archaeon (Archaeoglobus fulgidus). The CAA-adding enzyme consists of three main domains: N-terminal, Central, and C-terminal ones. The catalytic core located in the cleft between the N-terminal and Central domains. When we compare the conformations of class I and class II CCA-adding enzymes, we find that the catalytic cores are very similar in spite of the different overall folds. Both of the catalytic core consist of five beta strands and two alpha helices, and about 62 residues near the catalytic center can be superimposed well. Besides, Mg2+ ion(s) exists in each catalytic core, and both classes are similar in that three specific amino residues surround the Mg2+ ion. Thus it is expected that the catalytic cores of class I and class II enzymes originated from a common ancestor. On the other hand, the recognition mechanisms of substrate (ATP, CTP, tRNA) are different between these two classes. For example, when substrate approaches active pocket, conformational change is different between class I and class II enzymes. However, at this time, the details of substrate recognition mechanism have not been known well. It is expected that the studies of CCA-adding enzyme enable development of the enzyme for synthesizing an RNA of any base sequence without using a DNA template.
Protein Data Bank (PDB)
Okabe, M. Tomita, K. Ishitani, R. Ishii, R. Takeuchi, N. Arisaka, F. Nureki, O. Yokoyama, S.; "Divergent evolutions of trinucleotide polymerization revealed by an archaeal CCA-adding enzyme structure."; Embo J.; (2003) 22:5918-5927 PubMed:14592988.
author: Jun-ichi Ito