Group II intron

Group II intron is a class of intron found in rRNA, tRNA, mRNA of organelles in fungi, plants, protists, and mRNA in bacteria. Self-splicing occurs in vitro (for a few of the introns studied to date), but protein machinery is probably required in vivo. In contrast to group I introns, intron excision occurs in the absence of GTP and involves the formation of a lariat, with a branchpoint strongly resembling that found in lariats formed during splicing of nuclear pre-mRNA.

Structure and catalytic site
The secondary structure of group II introns is characterized by six typical stem-loop structures, also called domains I to VI or D1 to D6. The domains radiate from a central core that brings the 5' and 3' splice junctions into close proximity. The proximal helix structures of the six domains are connected by a few nucleotides in the central region (linker or joiner sequences). Due to its enormous size, the domain 1 was divided further into subdomains a, b, c, and d.

some anatomic and sequence differences of group II introns were identified which led to a further division into subgroups IIA and IIB.

Group II introns possess only a very few conserved nucleotides, and the nucleotides important for the catalytic function are spread over the complete intron structure. The few strictly conserved primary sequences are the consensus at the 5' and 3' splicing site (...↓GUGYG&... and ...AY↓...), some of the nucleotides of the central core (joiner sequences), a relatively high number of nucleotides of D5 and some short sequence stretches of D1. The unpaired adenosine in D6 marked by an asterisk (7 or 8 nt away from the 3' splicing site, respectively) is also conserved and plays a central role in the splicing process.

In 2005, AD. Lencastre et al. found that during splicing of Group II introns, all reactants are preorganized before the initiation of splicing. The branch site, both exons, the catalytically essential regions of D5 and J2/3, and epsilon−epsilon' are in close proximity before the first step of splicing occurs. In addition to the bulge and AGC triad regions of D5, the J2/3 linker region, the epsilon−epsilon' nucleotides and the coordination loop in D1 are crucial for the architecture and function of the active-site.