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.[1] 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.[2][3] Finally, their ability to site-specifically mobilize to new DNA sites has been exploited as a tool for biotechnology.

Structure and catalysis

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 DI to DVI. 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 I 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, IIB and IIC were identified, along with varying distance of the bulged adenosine in domain VI (the prospective branch point forming the lariat) from the 3' splice site, and the inclusion or omission of structural elements such as a coordination loop in domain I, which is present in IIB and IIC introns but not IIA.[1] 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↓..., with the Y representing a pyrimidine), some of the nucleotides of the central core (joiner sequences), a relatively high number of nucleotides of DV and some short-sequence stretches of DI. The unpaired adenosine in DVI (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. The 2' hydroxyl of the bulged adenosine attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. This results in a branched intron lariat connected by a 2' phosphodiester linkage at the DVI adenosine.

Protein machinery is required for splicing in vivo, and long-range intron-intron and intron-exon interactions are important for splice site positioning, as well as a number of tertiary contacts between motifs, including kissing-loop and tetraloop-receptor interactions. 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 DV and J2/3, and ε−ε' are in close proximity before the first step of splicing occurs. In addition to the bulge and AGC triad regions of DV, the J2/3 linker region, the ε−ε' nucleotides and the coordination loop in DI are crucial for the architecture and function of the active-site.[4]

The first crystal structure of a group II intron was resolved in 2008 for the Oceanobacillus iheyensis group IIC catalytic intron, and was joined by the Pylaiella littoralis (P.li.LSUI2) group IIB intron in 2014. Attempts have been made to model the tertiary structure of other group II introns, such as the ai5γ group IIB intron, using a combination of programs for homology mapping onto known structures and de novo modeling of previously unresolved regions.[5] Group IIC are characterized by a catalytic triad made up by CGC, while Group IIA and Group IIB are made up by AGC catalytic triad, which is more similar to the catalytic triad of the spliceosome. It is believed that the Group IIC are also smaller, more reactive and more ancient. The first step of splicing in Group IIC intron is done by water and it form a linear structure instead of lariat.[6]

Distribution and phylogeny

Group II introns are found in rRNA, tRNA, and mRNA of organelles (chloroplasts and mitochondria) in fungi, plants, and protists, and also in mRNA in bacteria. The first intron to be identified as distinct from group I was the ai5γ group IIB intron, which was isolated in 1986 from a pre-mRNA transcript of the oxi 3 mitochondrial gene of Saccharomyces cerevisiae.[7]

A subset of group II introns encode essential splicing proteins, known as intron-encoded proteins or IEPs, in intronic ORFs. The length of these introns can, as a result, be up to 3 kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps, with both also using magnesium ions to stabilize the leaving group in each step, which has led some to theorize a phylogenetic link between group II introns and the nuclear spliceosome. Further evidence for this link includes structural similarity between the U2/U6 junction of spliceosomal RNA and domain V of group II introns, which contains the catalytic AGC triad and much of the heart of the active site, as well as parity between conserved 5' and 3' end sequences.[8]

See also


  1. ^ a b Lambowitz AM, Zimmerly S (August 2011). "Group II introns: mobile ribozymes that invade DNA". Cold Spring Harbor Perspectives in Biology. 3 (8): a003616. doi:10.1101/cshperspect.a003616. PMC 3140690. PMID 20463000.
  2. ^ Seetharaman M, Eldho NV, Padgett RA, Dayie KT (February 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 1370903. PMID 16428604.
  3. ^ 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.
  4. ^ de Lencastre A, Hamill S, Pyle AM (July 2005). "A single active-site region for a group II intron". Nature Structural & Molecular Biology. 12 (7): 626–7. doi:10.1038/nsmb957. PMID 15980867.
  5. ^ Somarowthu S, Legiewicz M, Keating KS, Pyle AM (February 2014). "Visualizing the ai5γ group IIB intron". Nucleic Acids Research. 42 (3): 1947–58. doi:10.1093/nar/gkt1051. PMID 24203709.
  6. ^ Keating KS, Toor N, Perlman PS, Pyle AM (January 2010). "A structural analysis of the group II intron active site and implications for the spliceosome". RNA. 16 (1): 1–9. doi:10.1261/rna.1791310. PMC 2802019. PMID 19948765.
  7. ^ Peebles CL, Perlman PS, Mecklenburg KL, Petrillo ML, Tabor JH, Jarrell KA, Cheng HL (January 1986). "A self-splicing RNA excises an intron lariat". Cell. 44 (2): 213–23. doi:10.1016/0092-8674(86)90755-5. PMID 3510741.
  8. ^ Gordon PM, Sontheimer EJ, Piccirilli JA (February 2000). "Metal ion catalysis during the exon-ligation step of nuclear pre-mRNA splicing: extending the parallels between the spliceosome and group II introns". RNA. 6 (2): 199–205. PMID 10688359.

Further reading

External links

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


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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