Group II intron secondary structure
Group II ribozymes are divided into three families of secondary structure, IIA, IIB and IIC. IIA and IIB introns were originally distinguished based on group II introns in mitochondria and chloroplasts, and were further subdivided into IIA1, IIA2, IIB1 and IIB2 structures (Michel et al., 1989). The consensus structures based on the early data set continue to be useful (see links to the left). IIC introns were more recently recognized, and are only found in bacteria. For a consensus structure of IIC introns, see the link for Bacterial class C.
On the practical level, the three classes are distinguished by their modes of exon recognition. IIA introns recognize exons by the IBS1-EBS1, IBS2-EBS2 and δ-δ' pairings. IIB introns recognize exons by IBS1-EBS1, IBS2-EBS2 and IBS3-EBS3 pairings. IIC introns recognize exons by IBS1-EBS1 and IBS3-EBS3 (Michel&Westhof 2009 review; Pyle 2010 review).
In addition to IIA, IIB and IIC structures, it is useful to consider the secondary structures associated with each ORF phylogenetic class (see links to the left). ML introns have IIA1 secondary structures. CL1 and CL2 introns have IIB1 and IIB2 structures respectively, and bacterial class C have IIC structures. The remaining bacterial classes have IIB structures that vary from the originally defined IIB structures. Consensus structures are adapted from Toor et al., 2001 and Simon et al., 2008.