Summary: LAGLIDADG DNA endonuclease family
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Homing endonuclease Edit Wikipedia article
The homing endonucleases are a collection of endonucleases encoded either as freestanding genes within introns, as fusions with host proteins, or as self-splicing inteins. They catalyze the hydrolysis of genomic DNA within the cells that synthesize them, but do so at very few, or even singular, locations. Repair of the hydrolyzed DNA by the host cell frequently results in the gene encoding the homing endonuclease having been copied into the cleavage site, hence the term 'homing' to describe the movement of these genes. Homing endonucleases can thereby transmit their genes horizontally within a host population, increasing their allele frequency at greater than Mendelian rates.
Origin and mechanism
Although the origin and function of homing endonucleases is still being researched, the most established hypothesis considers them as selfish genetic elements, similar to transposons, because they facilitate the perpetuation of the genetic elements that encode them independent of providing a functional attribute to the host organism.
Homing endonuclease recognition sequences are long enough to occur randomly only with a very low probability (approximately once every ×109 bp), 7 and are normally found in one or very few instances per genome. Generally, owing to the homing mechanism, the gene encoding the endonuclease (the HEG, "homing endonuclease gene") is located within the recognition sequence which the enzyme cuts, thus interrupting the homing endonuclease recognition sequence and limiting DNA cutting only to sites that do not (yet) carry the HEG.
Prior to transmission, one allele carries the gene (HEG+) while the other does not (HEG−), and is therefore susceptible to being cut by the enzyme. Once the enzyme is synthesized, it breaks the chromosome in the HEG− allele, initiating a response from the cellular DNA repair system. The damage is repaired using recombination, taking the pattern of the opposite, undamaged DNA allele, HEG+, that contains the gene for the endonuclease. Thus, the gene is copied to the allele that initially did not have it and it is propagated through successive generations. This process is called "homing".
Homing endonucleases are always indicated with a prefix that identifies their genomic origin, followed by a hyphen: "I-" for homing endonucleases encoded within an intron, "PI-" (for "protein insert") for those encoded within an intein. Some authors have proposed using the prefix "F-" ("freestanding") for viral enzymes and other natural enzymes not encoded by introns nor inteins, and "H-" ("hybrid") for enzymes synthesized in a laboratory. Next, a capital letter is derived from the first letter of the name of the genus of the natural source organism, and two lower case letters are derived from the name of the species of that organism. Finally, a Roman numeral distinguishes different enzymes found in the same organism.
For example, we can mention the enzyme PI-TliII that is the second enzyme encoded by an intein found in the archaea Thermococcus litoralis, and H-DreI, the first synthetic homing endonuclease, created in a laboratory from the enzymes I-DmoI and I-CreI, taken respectively from Desulfurococcus mobilis and Chlamydomonas reinhardtii.
Comparison to restriction enzymes
- Whereas Type II restriction enzymes bind short, usually symmetric, recognition sequences of 4 to 8 bp, homing endonucleases bind very long and in many cases asymmetric recognition sequences spanning 12 to 40 bp.
- Homing endonucleases are generally more tolerant of substitutions in the recognition sequence. Minor variations in the recognition sequence usually decrease the activity of homing endonucleases, but often do not completely abolish it as often occurs with restriction enzymes.
- Homing endonucleases share structural motifs that suggest there are four families, whereas it has not been possible to determine simply recognisable and distinguishable families of Type II restriction enzymes.
- Homing endonucleases act as monomers or homodimers, and often require associated proteins to regulate their activity or form ribonucleoprotein complexes, wherein RNA is an integral component of the catalytic apparatus. Type II restriction enzymes can also function alone, as monomers or homodimers, or with additional protein subunits, but the accessory subunits differ from those of the homing endonucleases. Thus, they can require restriction, modification, and specificity subunits for their action.
- Finally, homing endonucleases have a broader phylogenetic distribution, occurring in all three biological domains—the archaea, bacteria and eukarya. Type II restriction enzymes occur only in archaea, bacteria and certain viruses. Homing endonucleases are also expressed in all three compartments of the eukaryotic cell: nuclei, mitochondria and chloroplasts. Open reading frames encoding homing endonucleases have been found in introns, inteins, and in freestanding form between genes, whereas genes encoding Type II restriction enzyme genes have been found only in freestanding form, almost always in close association with genes encoding cognate DNA modifying enzymes. Thus, while the Type II restriction enzymes and homing endonucleases share the function of cleaving double-stranded DNA, they appear to have evolved independently.
the structure and dna recognition of a bifunctional homing endonuclease and group i intron splicing factor
|LAGLIDADG DNA endonuclease family|
the homing endonuclease i-scei bound to its dna recognition region
- LAGLIDADG: Every polypeptide has 1 or 2 LAGLIDADG motifs. The sequence LAGLIDADG is a conserved sequence of amino acids where each letter is a code that identifies a specific residue. This sequence is directly involved in the DNA cutting process. Those enzymes that have only one motif work as homodimers, creating a saddle that interacts with the major groove of each DNA half-site. The LAGLIDADG motifs contribute amino acid residues to both the protein-protein interface between protein domains or subunits, and to the enzyme's active sites. Enzymes that possess two motifs in a single protein chain act as monomers, creating the saddle in a similar way. The first structures to be determined of homing endonucleases (of PI-SceI and I-CreI, both reported in 1997) were both from the LAGLIDADG structural family., The following year, the first structure of a homing endonuclease (I-CreI) bound to its DNA target site was also reported.
- GIY-YIG: These have only one GIY-YIG motif, in the N-terminal region, that interacts with the DNA in the cutting site. The prototypic enzyme of this family is I-TevI which acts as a monomer. Separate structural studies have been reported of the DNA-binding and catalytic domains of I-TevI, the former bound to its DNA target and the latter in the absence of DNA.,
- His-Cys box: These enzymes possess a region of 30 amino acids that includes 5 conserved residues: two histidines and three cysteins. They co-ordinate the metal cation needed for catalysis. I-PpoI is the best characterized enzyme of this family and acts as a homodimer. Its structure was reported in 1998.
- H-N-H: These have a consensus sequence of approximately 30 amino acids. It includes two pairs of conserved histidines and one asparagine that create a zinc finger domain. I-HmuI is the best characterized enzyme of this family, and acts as a monomer. Its structure was reported in 2004.
- PD-(D/E)xK: These enzymes contain a canonical nuclease catalytic domain typically found in type II restriction endonucleases. The best characterized enzyme in this family, I-Ssp6803I, acts as a tetramer. Its structure was reported in 2007.
- Vsr-like: These enzymes were discovered in the Global Ocean Sampling Metagenomic Database and first described in 2009. The term 'Vsr-like' refers to the presence of a C-terminal nuclease domain that displays recognizable homology to bacterial Very Short Patch Repair (Vsr) endonucleases.
crystal structure of pi-scei miniprecursor
crystal structure of pi-scei miniprecursor
The crystal structure of the homing endonuclease PI-Sce revealed two domains: an endonucleolytic centre resembling the C-terminal domain of Drosophila melanogaster Hedgehog protein, and a second domain (Homing endonuclease-associated Hint domain) containing the protein-splicing active site.
- REBASE, a comprehensive restriction enzyme database from New England Biolabs with links to related literature.
- List of homing endonuclease cutting sites
- I-CreI homing endonuclease
- Restriction enzyme
- Introns and inteins
- Intragenomic conflict: Homing endonuclease genes
- Edgell DR (February 2009). "Selfish DNA: homing endonucleases find a home". Curr Biol. 19 (3): R115–R117. doi:10.1016/j.cub.2008.12.019. PMID 19211047.
- Jasin M (Jun 1996). "Genetic manipulation of genomonth with rare-cutting endonucleases". Trends Genet. 12 (6): 224–8. doi:10.1016/0168-9525(96)10019-6. PMID 8928227.
- Burt A, Koufopanou V (December 2004). "Homing endonuclease genes: the rise and fall and rise again of a selfish element". Curr Opin Genet Dev. 14 (6): 609–15. doi:10.1016/j.gde.2004.09.010. PMID 15531154.
- Belfort M, Roberts RJ (September 1995). "Homing endonucleases: keeping the house in order". Nucleic Acids Res. 25 (17): 3379–88. doi:10.1093/nar/25.17.3379. PMC . PMID 9254693.
- Chevalier BS, Kortemme T, Chadsey MS, Baker D, Monnat RJ, Stoddard BL (October 2002). "Design, activity, and structure of a highly specific artificial endonuclease". Mol. Cell. 10 (4): 895–905. doi:10.1016/S1097-2765(02)00690-1. PMID 12419232.
- Hirata R, Ohsumk Y, Nakano A, Kawasaki H, Suzuki K, Anraku Y (April 1990). "Molecular structure of a gene, VMA1, encoding the catalytic subunit of H(+)-translocating adenosine triphosphatase from vacuolar membranes of Saccharomyces cerevisiae". J Biol Chem. 265 (12): 6726–33. PMID 2139027.
- Kane PM, Yamashiro CT, Wolczyk DF, Neff N, Goebl M, Stevens TH (November 1990). "Protein splicing converts the yeast TFP1 gene product to the 69-kD subunit of the vacuolar H(+)-adenosine triphosphatase". Science. 250 (4981): 651–7. doi:10.1126/science.2146742. PMID 2146742.
- Perler FB, Comb DG, Jack WE, Moran LS, Qiang B, Kucera RB, Benner J, Slatko BE, Nwankwo DO, Hempstead SK, Carlow CK, Jannasch H (June 1992). "Intervening sequences in an Archaea DNA polymerase gene". PNAS. 89 (12): 5577–81. doi:10.1073/pnas.89.12.5577. PMC . PMID 1608969.
- Jurica MS, Monnat RJ, Stoddard BL (October 1998). "DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-CreI" (PDF). Mol. Cell. 2 (4): 469–76. doi:10.1016/S1097-2765(00)80146-X. PMID 9809068.
- Gimble FS, Wang J (October 1996). "Substrate recognition and induced DNA distortion by the PI-SceI endonuclease, an enzyme generated by protein splicing". J Mol Biol. 263 (2): 163–80. doi:10.1006/jmbi.1996.0567. PMID 8913299.
- Argast GM, Stephens KM, Emond MJ, Monnat RJ (July 1998). "I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential in vitro enrichment". J Mol Biol. 280 (3): 345–53. doi:10.1006/jmbi.1998.1886. PMID 9665841.
- Shibata T, Nakagawa K, Morishima N (1995). "Multi-site-specific endonucleases and the initiation of homologous genetic recombination in yeast". Adv Biophys. 31: 77–91. doi:10.1016/0065-227X(95)99384-2. PMID 7625280.
- Zimmerly S, Guo H, Eskes R, Yang J, Perlman PS, Lambowitz AM (November 1995). "A group II intron RNA is a catalytic component of a DNA endonuclease involved in intron mobility". Cell. 83 (4): 529–38. doi:10.1016/0092-8674(95)90092-6. PMID 7585955.
- Linn, Stuart M; Lloyd, R Stephen; Roberts, Richard J (December 1993). Nucleases. Cold Spring Harbor Press. pp. 35–88. ISBN 978-0-87969-426-5.
- Linn, Stuart M; Lloyd, R Stephen; Roberts, Richard J (December 1993). Nucleases. Cold Spring Harbor Press. pp. 89–109. ISBN 978-0-87969-426-5.
- Roberts RJ, Macelis D (January 1997). "REBASE-restriction enzymes and methylases". Nucleic Acids Res. 25 (1): 248–62. doi:10.1093/nar/25.1.248. PMC . PMID 9016548.
- Lambowitz AM, Belfort M (1993). "Introns as mobile genetic elements". Annu Rev Biochem. 62: 587–622. doi:10.1146/annurev.bi.62.070193.003103. PMID 8352597.
- Linn, Stuart M; Lloyd, R Stephen; Roberts, Richard J (December 1993). Nucleases. Cold Spring Harbor Press. pp. 111–143. ISBN 978-0-87969-426-5.
- Wilson GG (December 1988). "Cloned restriction-modification systems—a review". Gene. 74 (1): 281–9. doi:10.1016/0378-1119(88)90304-6. PMID 3074014.
- Heath, P.; et al. (June 1997). "The structure of I-Crel, a group I intron-encoded homing endonuclease". Nature Structural Biology. 4 (6): 468–476. doi:10.1038/nsb0697-468. PMID 9187655.
- Duan, X. (May 1997). "Crystal structure of PI-SceI, a homing endonuclease with protein splicing activity". Cell. 89 (4): 555–564. doi:10.1016/S0092-8674(00)80237-8. PMID 9160747.
- Van Roey, P.; Fox, KM; et al. (July 2001). "Intertwined structure of the DNA-binding domain of intron endonuclease I-TevI with its substrate". EMBO J. 20 (14): 3631–3637. doi:10.1093/emboj/20.14.3631. PMC . PMID 11447104.
- Van Roey, P.; Kowalski, Joseph C.; et al. (July 2002). "Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI". Nature Structural Biology. 9 (11): 806–811. doi:10.1038/nsb853. PMID 12379841.
- Flick, K.; et al. (July 1998). "DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI". Nature. 394 (6688): 96–101. doi:10.1038/27952. PMID 9665136.
- Shen, B.W.; et al. (September 2004). "DNA binding and cleavage by the HNH homing endonuclease I-HmuI". J. Mol. Biol. 342 (1): 43–56. doi:10.1016/j.jmb.2004.07.032. PMID 15313606.
- Zhao, L.; et al. (May 2007). "The restriction fold turns to the dark side: a bacterial homing endonuclease with a PD-(D/E)-XK motif". EMBO Journal. 26 (9): 2432–2442. doi:10.1038/sj.emboj.7601672. PMC . PMID 17410205.
- Dassa, B.; et al. (March 2009). "Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family". Nucleic Acids Research. 37 (8): 2560–2573. doi:10.1093/nar/gkp095. PMC . PMID 19264795.
- Moure CM, Gimble FS, Quiocho FA (October 2002). "Crystal structure of the intein homing endonuclease PI-SceI bound to its recognition sequence". Nat. Struct. Biol. 9 (10): 764–70. doi:10.1038/nsb840. PMID 12219083.
- Perler FB. "InBase". Archived from the original on 2010-08-02. Retrieved 2010-08-09.
The Intein Database and Registry (from New England Biolabs)
- Perler FB (January 2002). "InBase: the Intein Database". Nucleic Acids Res. 30 (1): 383–4. doi:10.1093/nar/30.1.383. PMC . PMID 11752343.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
LAGLIDADG DNA endonuclease family Provide feedback
This is a family of site-specific DNA endonucleases encoded by DNA mobile elements. Similar to PF00961 the members of this family are also LAGLIDADG endonucleases.
Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, Mian IS; , Nucleic Acids Res 1997;25:4626-4638.: Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. PUBMED:9358175 EPMC:9358175
Internal database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004860Homing endonucleases (HEnases) form a large and highly diverse class of proteins encoded by introns and inteins that confer mobility to their host genetic elements. LAGLIDADG HEnases are structured into two tandemly repeated homing endonuclease-like domains [PUBMED:17603302, PUBMED:8918801]. This entry represents the homing endonuclease LAGLIDADG domain [PUBMED:9358175].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||endonuclease activity (GO:0004519)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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This superfamily includes a variety of LAGLIDADG-like homing endonuclease like families.
The clan contains the following 7 members:Endonuc_subdom Hom_end LAGLIDADG_1 LAGLIDADG_2 LAGLIDADG_3 LAGLIDADG_WhiA WhiA_N
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
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- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Seed source:||Pfam-B_3225 (release 6.5)|
|Number in seed:||43|
|Number in full:||484|
|Average length of the domain:||160.80 aa|
|Average identity of full alignment:||23 %|
|Average coverage of the sequence by the domain:||41.10 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||13|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the LAGLIDADG_2 domain has been found. There are 8 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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