3  structures 0  species 0  sequences

Motif: Domain-V (RM00007)

Description: Splicing domain V


Wikipedia annotation Edit Wikipedia article

The Rfam group coordinates the annotation of Rfam data in Wikipedia. This motif is described by a Wikipedia entry entitled Group II intron. More...

Structure of group II intron

Group II introns are a large class of self-catalytic ribozymes and mobile genetic elements found within the genes of all three domains of life. Ribozyme activity (e.g., self-splicing) can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing[citation needed]. In contrast to group I introns, intron excision occurs in the absence of GTP and involves the formation of a lariat, with an A-residue branchpoint strongly resembling that found in lariats formed during splicing of nuclear pre-mRNA. It is hypothesized that pre-mRNA splicing (see spliceosome) may have evolved from group II introns, due to the similar catalytic mechanism as well as the structural similarity of the Domain V substructure to the U6/U2 extended snRNA.[1][2] Finally, their ability to site-specifically mobilize to new DNA sites has been exploited as a tool for biotechnology.

Structure and catalytic site

The Domain V substructure that is shared between Group II introns and U6 spliceosomal RNA.

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. Sequence differences of group II introns that led to a further division into subgroups IIA and IIB were identified. Group II introns also form very complicated RNA Tertiary Structure.

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 in the figure and located 7 or 8 nt away from the 3' splicing site) is also conserved and plays a central role in the splicing process.

In 2005, A. De 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.

Group II catalytic intron

Group II catalytic introns are found in rRNA, tRNA, and mRNA of organelles (chloroplasts and mitochondria) in fungi, plants, and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). This model and alignment represents only domains V and VI. A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can, therefore, be up to 3 kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long-range intron-intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB, which differ in splice site consensus, and the distance of the bulged adenosine in domain VI (the prospective branch point forming the lariat) from the 3' splice site.

See also


  1. ^ Seetharaman, M; Eldho, NV; Padgett, RA; Dayie, KT (Feb 2006). "Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA". RNA. 12 (2): 235–47. doi:10.1261/rna.2237806. PMC 1370903Freely accessible. PMID 16428604. 
  2. ^ Valadkhan, S (May–Jun 2010). "Role of the snRNAs in spliceosomal active site". RNA biology. 7 (3): 345–53. doi:10.4161/rna.7.3.12089. PMID 20458185. 

External links

This page is based on a wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.


You can either download the motif alignment or view it directly in your browser window. More...

Formatting options

You can view or download motif alignments in several formats. Check either the "download" button, to save the formatted alignment, or "view", to see it in your browser window, and click "Generate".

Alignment format:


There are 3 PDB entires which have been used to build the motif model.

The table of results below may be sorted by clicking on the column titles, or restored to the original order here.

Original order PDB ID PDB chain ID PDB Residues
2 1kxk A -
2 1r2p A -
2 1xhp A -

Family matches

There are 18 Rfam families which match this motif.

This section shows the families which have been annotated with this motif. Users should be aware that the motifs are structural constructs and do not necessarily conform to taxonomic boundaries in the way that Rfam families do. More...

Original order Family Accession Family Description Number of Hits Fraction of Hits Sum of Bits Image
3 RF00011 Bacterial RNase P class B 16 0.140 174.9 Match Image
3 RF00018 CsrB/RsmB RNA family 19 0.500 202.5 Match Image
3 RF00026 U6 spliceosomal RNA 172 0.915 3759.8 Match Image
3 RF00029 Group II catalytic intron 92 1.000 3204.8 Match Image
3 RF00300 Small nucleolar RNA Z221/R21b 2 0.167 22.1 Match Image
3 RF00413 Small nucleolar RNA SNORA19 2 0.059 27.6 Match Image
3 RF00449 HIF-1 alpha IRES 6 0.353 73.6 Match Image
3 RF00553 Small Cajal body specific RNA 1 4 0.138 44.2 Match Image
3 RF00724 microRNA mir-282 2 0.133 20.2 Match Image
3 RF01071 Ornate Large Extremophilic RNA 2 0.100 27.8 Match Image
3 RF01699 Clostridiales-1 RNA 20 0.103 255.8 Match Image
3 RF01749 pan motif 8 0.108 95.6 Match Image
3 RF02356 Alphaproteobacterial sRNA BjrC1505 2 0.080 22.3 Match Image
3 RF02384 FasX small RNA 2 0.250 20.4 Match Image
3 RF02540 Archaeal large subunit ribosomal RNA 16 0.176 236.7 Match Image
3 RF02541 Bacterial large subunit ribosomal RNA 21 0.206 258.2 Match Image
3 RF02542 Microsporidia small subunit ribosomal RNA 6 0.130 64.8 Match Image
3 RF02543 Eukaryotic large subunit ribosomal RNA 23 0.261 295.7 Match Image


This section shows the database cross-references that we have for this Rfam motif.

Literature references

  1. Seetharaman M, Eldho NV, Padgett RA, Dayie KT RNA. 2006;12:235-47. Structure of a self-splicing group II intron catalytic effector domain 5: parallels with spliceosomal U6 RNA. PUBMED:16428604

  2. Valadkhan S RNA Biol. ;7:345-53. Role of the snRNAs in spliceosomal active site. PUBMED:20458185

External database links

Curation and motif details

This section shows the detailed information about the Rfam motif. We're happy to receive updated or improved alignments for new or existing families. Submit your new alignment and we'll take a look.


Seed source CMfinder
Structure source N/A
Type Stem Loop
Author Gardner PP
Alignment details
Alignment Number of
Average length Sequence
identity (%)
seed 62 33.26 53

Model information

Build commands
cmbuild -F CM SEED
cmcalibrate CM
Gathering cutoff 10.0
Covariance model Download the Infernal CM for the motif here