The homing endonucleases are a special type of restriction enzymes encoded by introns or inteins. They act on the cellular DNA of the cell that synthesizes them; to be precise, in the opposite allele of the gene that encode them.[1]
The list includes some of the most studied examples. The following concepts have been detailed:
H1
: LAGLIDADG family – H2
: GIY-YIG family – H3
: H-N-H family – H4
: His-Cys box family – H5
: PD-(D/E)xK – H6
: EDxHD. (Further reading: .)Enzyme | SF | PDB code | Source | D | SCL | Recognition sequence | Cut | |
---|---|---|---|---|---|---|---|---|
I-AniI[2] | H1 | Aspergillus nidulans | E | mito | 5' TTGAGGAGGTTTCTCTGTAAATAA 3' AACTCCTCCAAAGAGACATTTATT | 5' ---TTGAGGAGGTTTC {{Pad|2em}} TCTGTAAATAA--- 3' 3' ---AACTCCTCC {{Pad|2em}} AAAGAGACATTTATT--- 5' | ||
I-CeuI[3] [4] [5] [6] | H1 | Chlamydomonas eugametos | E | chloro | 5' TAACTATAACGGTCCTAAGGTAGCGA 3' ATTGATATTGCCAGGATTCCATCGCT | 5' ---TAACTATAACGGTCCTAA {{Pad|2em}} GGTAGCGA--- 3' 3' ---ATTGATATTGCCAG {{Pad|2em}} GATTCCATCGCT--- 5' | ||
I-ChuI[7] [8] | H1 | Chlamydomonas humicola | E | chloro | 5' GAAGGTTTGGCACCTCGATGTCGGCTCATC 3' CTTCCAAACCGTGGAGCTACAGCCGAGTAG | 5' ---GAAGGTTTGGCACCTCG {{Pad|2em}} ATGTCGGCTCATC--- 3' 3' ---CTTCCAAACCGTG {{Pad|2em}} GAGCTACAGCCGAGTAG--- 5' | ||
I-CpaI[9] | H1 | Chlamydomonas pallidostigmata | E | chloro | 5' CGATCCTAAGGTAGCGAAATTCA 3' GCTAGGATTCCATCGCTTTAAGT | 5' ---CGATCCTAAGGTAGCGAA {{Pad|2em}} ATTCA--- 3' 3' ---GCTAGGATTCCATC {{Pad|2em}} GCTTTAAGT--- 5' | ||
I-CpaII[10] | H1 | Chlamydomonas pallidostigmata | E | chloro | 5' CCCGGCTAACTCTGTGCCAG 3' GGGCCGATTGAGACACGGTC | 5' ---CCCGGCTAACTC {{Pad|2em}} TGTGCCAG--- 3' 5' ---GGGCCGAT {{Pad|2em}} TGAGACACGGTC--- 3' | ||
I-CreI[11] | H1 | Chlamydomonas reinhardtii | E | chloro | 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG 3' GACCCAAGTTTTGCAGCACTCTGTCAAACC | 5' ---CTGGGTTCAAAACGTCGTGA {{Pad|2em}} GACAGTTTGG--- 3' 3' ---GACCCAAGTTTTGCAG {{Pad|2em}} CACTCTGTCAAACC--- 5' | ||
I-DmoI | H1 | Desulfurococcus mobilis | A | chrm | 5' ATGCCTTGCCGGGTAAGTTCCGGCGCGCAT 3' TACGGAACGGCCCATTCAAGGCCGCGCGTA | 5' ---ATGCCTTGCCGGGTAA {{Pad|2em}} GTTCCGGCGCGCAT--- 3' 3' ---TACGGAACGGCC {{Pad|2em}} CATTCAAGGCCGCGCGTA--- 5' | ||
H-DreI[12] | H1 | Hybrid: I-DmoI and I-CreI | AE | 5' CAAAACGTCGTAAGTTCCGGCGCG 3' GTTTTGCAGCATTCAAGGCCGCGC | 5' ---CAAAACGTCGTAA {{Pad|2em}} GTTCCGGCGCG--- 3' 3' ---GTTTTGCAG {{Pad|2em}} CATTCAAGGCCGCGC--- 5' | |||
I-HmuI[13] [14] | H3 | Bacillus subtilis phage SP01 | B | phage | 5' AGTAATGAGCCTAACGCTCAGCAA 3' TCATTACTCGGATTGCGAGTCGTT | Nicking endonuclease: * {{Pad|2em}} 3' ---TCATTACTCGGATTGC {{Pad|2em}} GAGTCGTT--- 5' | ||
I-HmuII[15] | H3 | Bacillus subtilis phage SP82 | B | phage | 5' AGTAATGAGCCTAACGCTCAACAA 3' TCATTACTCGGATTGCGAGTTGTT | Nicking endonuclease: * {{Pad|2em}} 3' ---TCATTACTCGGATTGCGAGTTGTTN<sub>35</sub> {{Pad|2em}} NNNN--- 5' | ||
I-LlaI[16] [17] | H3 | Lactococcus lactis | B | chrm | 5' CACATCCATAACCATATCATTTTT 3' GTGTAGGTATTGGTATAGTAAAAA | 5' ---CACATCCATAA {{Pad|2em}} CCATATCATTTTT--- 3' 3' ---GTGTAGGTATTGGTATAGTAA {{Pad|2em}} AAA--- 5' | ||
I-MsoI | H1 | Monomastix sp. | E | 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG 3' GACCCAAGTTTTGCAGCACTCTGTCAAACC | 5' ---CTGGGTTCAAAACGTCGTGA {{Pad|2em}} GACAGTTTGG--- 3' 3' ---GACCCAAGTTTTGCAG {{Pad|2em}} CACTCTGTCAAACC--- 5' | |||
PI-PfuI | H1 | Pyrococcus furiosus Vc1 | 5' GAAGATGGGAGGAGGGACCGGACTCAACTT 3' CTTCTACCCTCCTCCCTGGCCTGAGTTGAA | 5' ---GAAGATGGGAGGAGGG {{Pad|2em}} ACCGGACTCAACTT--- 3' 3' ---CTTCTACCCTCC {{Pad|2em}} TCCCTGGCCTGAGTTGAA--- 5' | ||||
PI-PkoII | H1 | Pyrococcus kodakarensis BAA-918 | A | 5' CAGTACTACGGTTAC 3' GTCATGATGCCAATG | 5' ---CAGTACTACG{{Pad|2em}} GTTAC--- 3' 3' ---GTCATG {{Pad|2em}}ATGCCAATG--- 5' | |||
I-PorI[18] [19] | H3 | Pyrobaculum organotrophum | A | chrm | 5' GCGAGCCCGTAAGGGTGTGTACGGG 3' CGCTCGGGCATTCCCACACATGCCC | 5' ---GCGAGCCCGTAAGGGT {{Pad|2em}} GTGTACGGG--- 3' 3' ---CGCTCGGGCATT {{Pad|2em}} CCCACACATGCCC--- 5' | ||
I-PpoI | H4 | Physarum polycephalum | E | plasmid | 5' TAACTATGACTCTCTTAAGGTAGCCAAAT 3' ATTGATACTGAGAGAATTCCATCGGTTTA | 5' ---TAACTATGACTCTCTTAA {{Pad|2em}} GGTAGCCAAAT--- 3' 3' ---ATTGATACTGAGAG {{Pad|2em}} AATTCCATCGGTTTA--- 5' | ||
PI-PspI | H1 | Pyrococcus sp. | A | chrm | 5' TGGCAAACAGCTATTATGGGTATTATGGGT 3' ACCGTTTGTCGATAATACCCATAATACCCA | 5' ---TGGCAAACAGCTATTAT {{Pad|2em}} GGGTATTATGGGT--- 3' 3' ---ACCGTTTGTCGAT {{Pad|2em}} AATACCCATAATACCCA--- 5' | ||
I-ScaI[20] [21] | H1 | Saccharomyces capensis | E | mito | 5' TGTCACATTGAGGTGCACTAGTTATTAC 3' ACAGTGTAACTCCACGTGATCAATAATG | 5' ---TGTCACATTGAGGTGCACT {{Pad|2em}} AGTTATTAC--- 3' 3' ---ACAGTGTAACTCCAC {{Pad|2em}} GTGATCAATAATG--- 5' | ||
I-SceI | H1 | Saccharomyces cerevisiae | E | mito | 5' AGTTACGCTAGGGATAACAGGGTAATATAG 3' TCAATGCGATCCCTATTGTCCCATTATATC | 5' ---AGTTACGCTAGGGATAA {{Pad|2em}} CAGGGTAATATAG--- 3' 3' ---TCAATGCGATCCC {{Pad|2em}} TATTGTCCCATTATATC--- 5' | ||
PI-SceI[22] [23] | H1 | Saccharomyces cerevisiae | 5' ATCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGGCA 3' TAGATACAGCCCACGCCTCTTTCTCCATTACTTTACCGT | 5' ---ATCTATGTCGGGTGC {{Pad|2em}} GGAGAAAGAGGTAATGAAATGGCA--- 3' 3' ---TAGATACAGCC {{Pad|2em}} CACGCCTCTTTCTCCATTACTTTACCGT--- 5' | ||||
I-SceII[24] [25] [26] | H1 | Saccharomyces cerevisiae | E | mito | 5' TTTTGATTCTTTGGTCACCCTGAAGTATA 3' AAAACTAAGAAACCAGTGGGACTTCATAT | 5' ---TTTTGATTCTTTGGTCACCC {{Pad|2em}} TGAAGTATA--- 3' 3' ---AAAACTAAGAAACCAG {{Pad|2em}} TGGGACTTCATAT--- 5' | ||
I-SecIII[27] [28] | H1 | Saccharomyces cerevisiae | E | mito | 5' ATTGGAGGTTTTGGTAACTATTTATTACC 3' TAACCTCCAAAACCATTGATAAATAATGG | 5' ---ATTGGAGGTTTTGGTAAC {{Pad|2em}} TATTTATTACC--- 3' 3' ---TAACCTCCAAAACC {{Pad|2em}} ATTGATAAATAATGG--- 5' | ||
I-SceIV[29] [30] | H1 | Saccharomyces cerevisiae | E | mito | 5' TCTTTTCTCTTGATTAGCCCTAATCTACG 3' AGAAAAGAGAACTAATCGGGATTAGATGC | 5' ---TCTTTTCTCTTGATTA {{Pad|2em}} GCCCTAATCTACG--- 3' 3' ---AGAAAAGAGAAC {{Pad|2em}} TAATCGGGATTAGATGC--- 5' | ||
I-SceV[31] | H3 | Saccharomyces cerevisiae | E | mito | 5' AATAATTTTCTTCTTAGTAATGCC 3' TTATTAAAAGAAGAATCATTACGG | 5' ---AATAATTTTCT {{Pad|2em}} TCTTAGTAATGCC--- 3' 3' ---TTATTAAAAGAAGAATCATTA {{Pad|2em}} CGG--- 5' | ||
I-SceVI[32] | H3 | Saccharomyces cerevisiae | E | mito | 5' GTTATTTAATGTTTTAGTAGTTGG 3' CAATAAATTACAAAATCATCAACC | 5' ---GTTATTTAATG {{Pad|2em}} TTTTAGTAGTTGG--- 3' 3' ---CAATAAATTACAAAATCATCA {{Pad|2em}} ACC--- 5' | ||
I-SceVII | H1 | Saccharomyces cerevisiae | E | mito | 5' TGTCACATTGAGGTGCACTAGTTATTAC 3' ACAGTGTAACTCCACGTGATCAATAATG | Unknown ** | ||
I-Ssp6803I | H5 | Synechocystis sp. PCC 6803 | B | 5' GTCGGGCTCATAACCCGAA 3' CAGCCCGAGTATTGGGCTT | 5' ---GTCGGGCT {{Pad|2em}} CATAACCCGAA--- 3' 3' ---CAGCCCGAGTA {{Pad|2em}} TTGGGCTT--- 5' | |||
I-TevI[33] [34] [35] | H2 | Escherichia coli phage T4 | B | phage | 5' AGTGGTATCAACGCTCAGTAGATG 3' TCACCATAGT TGCGAGTCATCTAC | 5' ---AGTGGTATCAAC {{Pad|2em}} GCTCAGTAGATG--- 3' 3' ---TCACCATAGT {{Pad|2em}} TGCGAGTCATCTAC--- 5' | ||
I-TevII[36] | H2 | Escherichia coli phage T4 | B | phage | 5' GCTTATGAGTATGAAGTGAACACGTTATTC 3' CGAATACTCATACTTCACTTGTGCAATAAG | 5' ---GCTTATGAGTATGAAGTGAACACGT {{Pad|2em}} TATTC--- 3' 3' ---CGAATACTCATACTTCACTTGTG {{Pad|2em}} CAATAAG--- 5' | ||
I-TevIII[37] | H3 | Escherichia coli phage RB3 | B | phage | 5' TATGTATCTTTTGCGTGTACCTTTAACTTC 3' ATACATAGAAAACGCACATGGAAATTGAAG | 5' ---T {{Pad|2em}} ATGTATCTTTTGCGTGTACCTTTAACTTC--- 3' 3' ---AT {{Pad|2em}} ACATAGAAAACGCACATGGAAATTGAAG--- 5' | ||
PI-TliI[38] [39] | H1 | Thermococcus litoralis | A | chrm | 5' TAYGCNGAYACNGACGGYTTYT 3' ATRCGNCTRTGNCTGCCTAARA | 5' ---TAYGCNGAYACNGACGG {{Pad|2em}} YTTYT--- 3' 3' ---ATRCGNCTRTGNC {{Pad|2em}} TGCCTAARA--- 5' | ||
PI-TliII[40] | H1 | Thermococcus litoralis | A | chrm | 5' AAATTGCTTGCAAACAGCTATTACGGCTAT 3' TTTAACGAACGTTTGTCGATAATGCCGATA | Unknown ** | ||
I-Tsp061I | H1 | Thermoproteus sp. IC-061 | A | 5' CTTCAGTATGCCCCGAAAC 3' GAAGTCATACGGGGCTTTG | 5' ---CTTCAGTAT {{Pad|2em}} GCCCCGAAAC--- 3' 3' ---GAAGT {{Pad|2em}} CATACGGGGCTTTG--- 5' | |||
I-Vdi141I | H1 | Vulcanisaeta distributa IC-141 | A | 5' CCTGACTCTCTTAAGGTAGCCAAA 3' GGACTGAGAGAATTCCATCGGTTT | 5' ---CCTGACTCTCTTAA {{Pad|2em}} GGTAGCCAAA--- 3' 3' ---GGACTGAG {{Pad|2em}} AGAATTCCATCGGTTT--- 5' |
*: Nicking endonuclease: These enzymes cut only one DNA strand, leaving the other strand untouched.
**: Unknown cutting site: Researchers have not been able to determine the exact cutting site of these enzymes yet.
Databases and lists of restriction enzymes:
Databases of proteins: