Legend of nucleobases | |
---|---|
Code | Nucleotide represented |
A | Adenine (A) |
C | Cytosine (C) |
G | Guanine (G) |
T | Thymine (T) |
N | A, C, G or T |
M | A or C |
R | A or G |
W | A or T |
Y | C or T |
S | C or G |
K | G or T |
H | A, C or T |
B | C, G or T |
V | A, C or G |
D | A, G or T |
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: Homing endonuclease § Structural families.)Enzyme | SF | PDB code | Source | D | SCL | Recognition sequence | Cut |
---|---|---|---|---|---|---|---|
I-AniI[2] | H1
|
1P8K | Aspergillus nidulans | E | mito | 5' TTGAGGAGGTTTCTCTGTAAATAA 3' AACTCCTCCAAAGAGACATTTATT
|
5' ---TTGAGGAGGTTTC TCTGTAAATAA--- 3' 3' ---AACTCCTCC AAAGAGACATTTATT--- 5'
|
I-CeuI[3][4][5][6] | H1
|
2EX5 | Chlamydomonas eugametos | E | chloro | 5' TAACTATAACGGTCCTAAGGTAGCGA 3' ATTGATATTGCCAGGATTCCATCGCT
|
5' ---TAACTATAACGGTCCTAA GGTAGCGA--- 3' 3' ---ATTGATATTGCCAG GATTCCATCGCT--- 5'
|
I-ChuI[7][8] | H1
|
Q32001 | Chlamydomonas humicola | E | chloro | 5' GAAGGTTTGGCACCTCGATGTCGGCTCATC 3' CTTCCAAACCGTGGAGCTACAGCCGAGTAG
|
5' ---GAAGGTTTGGCACCTCG ATGTCGGCTCATC--- 3' 3' ---CTTCCAAACCGTG GAGCTACAGCCGAGTAG--- 5'
|
I-CpaI[8][9] | H1
|
Q39562 | Chlamydomonas pallidostigmata | E | chloro | 5' CGATCCTAAGGTAGCGAAATTCA 3' GCTAGGATTCCATCGCTTTAAGT
|
5' ---CGATCCTAAGGTAGCGAA ATTCA--- 3' 3' ---GCTAGGATTCCATC GCTTTAAGT--- 5'
|
I-CpaII[10] | H1
|
Q39559 | Chlamydomonas pallidostigmata | E | chloro | 5' CCCGGCTAACTCTGTGCCAG 3' GGGCCGATTGAGACACGGTC
|
5' ---CCCGGCTAACTC TGTGCCAG--- 3' 5' ---GGGCCGAT TGAGACACGGTC--- 3'
|
I-CreI[11] | H1
|
1BP7 | Chlamydomonas reinhardtii | E | chloro | 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG 3' GACCCAAGTTTTGCAGCACTCTGTCAAACC
|
5' ---CTGGGTTCAAAACGTCGTGA GACAGTTTGG--- 3' 3' ---GACCCAAGTTTTGCAG CACTCTGTCAAACC--- 5'
|
I-DmoI | H1
|
1B24 | Desulfurococcus mobilis | A | chrm | 5' ATGCCTTGCCGGGTAAGTTCCGGCGCGCAT 3' TACGGAACGGCCCATTCAAGGCCGCGCGTA
|
5' ---ATGCCTTGCCGGGTAA GTTCCGGCGCGCAT--- 3' 3' ---TACGGAACGGCC CATTCAAGGCCGCGCGTA--- 5'
|
H-DreI[12] | H1
|
1MOW | Hybrid: I-DmoI and I-CreI | AE | 5' CAAAACGTCGTAAGTTCCGGCGCG 3' GTTTTGCAGCATTCAAGGCCGCGC
|
5' ---CAAAACGTCGTAA GTTCCGGCGCG--- 3' 3' ---GTTTTGCAG CATTCAAGGCCGCGC--- 5'
| |
I-HmuI[13][14] | H3
|
1U3E | Bacillus subtilis phage SP01 | B | phage | 5' AGTAATGAGCCTAACGCTCAGCAA 3' TCATTACTCGGATTGCGAGTCGTT
|
Nicking endonuclease: * 3' ---TCATTACTCGGATTGC GAGTCGTT--- 5'
|
I-HmuII[14][15] | H3
|
Q38137 | Bacillus subtilis phage SP82 | B | phage | 5' AGTAATGAGCCTAACGCTCAACAA 3' TCATTACTCGGATTGCGAGTTGTT
|
Nicking endonuclease: * 3' ---TCATTACTCGGATTGCGAGTTGTTN35 NNNN--- 5'
|
I-LlaI[16][17] | H3
|
P0A3U1 | Lactococcus lactis | B | chrm | 5' CACATCCATAACCATATCATTTTT 3' GTGTAGGTATTGGTATAGTAAAAA
|
5' ---CACATCCATAA CCATATCATTTTT--- 3' 3' ---GTGTAGGTATTGGTATAGTAA AAA--- 5'
|
I-MsoI | H1
|
1M5X | Monomastix sp. | E | 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG 3' GACCCAAGTTTTGCAGCACTCTGTCAAACC
|
5' ---CTGGGTTCAAAACGTCGTGA GACAGTTTGG--- 3' 3' ---GACCCAAGTTTTGCAG CACTCTGTCAAACC--- 5'
| |
PI-PfuI | H1
|
1DQ3 | Pyrococcus furiosus Vc1 | A | 5' GAAGATGGGAGGAGGGACCGGACTCAACTT 3' CTTCTACCCTCCTCCCTGGCCTGAGTTGAA
|
5' ---GAAGATGGGAGGAGGG ACCGGACTCAACTT--- 3' 3' ---CTTCTACCCTCC TCCCTGGCCTGAGTTGAA--- 5'
| |
PI-PkoII | H1
|
2CW7 | Pyrococcus kodakarensis BAA-918 | A | 5' CAGTACTACGGTTAC 3' GTCATGATGCCAATG
|
5' ---CAGTACTACG GTTAC--- 3' 3' ---GTCATG ATGCCAATG--- 5'
| |
I-PorI[18][19] | H3
|
Pyrobaculum organotrophum | A | chrm | 5' GCGAGCCCGTAAGGGTGTGTACGGG 3' CGCTCGGGCATTCCCACACATGCCC
|
5' ---GCGAGCCCGTAAGGGT GTGTACGGG--- 3' 3' ---CGCTCGGGCATT CCCACACATGCCC--- 5'
| |
I-PpoI | H4
|
1EVX | Physarum polycephalum | E | plasmid | 5' TAACTATGACTCTCTTAAGGTAGCCAAAT 3' ATTGATACTGAGAGAATTCCATCGGTTTA
|
5' ---TAACTATGACTCTCTTAA GGTAGCCAAAT--- 3' 3' ---ATTGATACTGAGAG AATTCCATCGGTTTA--- 5'
|
PI-PspI | H1
|
Q51334 | Pyrococcus sp. | A | chrm | 5' TGGCAAACAGCTATTATGGGTATTATGGGT 3' ACCGTTTGTCGATAATACCCATAATACCCA
|
5' ---TGGCAAACAGCTATTAT GGGTATTATGGGT--- 3' 3' ---ACCGTTTGTCGAT AATACCCATAATACCCA--- 5'
|
I-ScaI[20][21] | H1
|
P03873 | Saccharomyces capensis | E | mito | 5' TGTCACATTGAGGTGCACTAGTTATTAC 3' ACAGTGTAACTCCACGTGATCAATAATG
|
5' ---TGTCACATTGAGGTGCACT AGTTATTAC--- 3' 3' ---ACAGTGTAACTCCAC GTGATCAATAATG--- 5'
|
I-SceI[4][5] | H1
|
1R7M | Saccharomyces cerevisiae | E | mito | 5' AGTTACGCTAGGGATAACAGGGTAATATAG 3' TCAATGCGATCCCTATTGTCCCATTATATC
|
5' ---AGTTACGCTAGGGATAA CAGGGTAATATAG--- 3' 3' ---TCAATGCGATCCC TATTGTCCCATTATATC--- 5'
|
PI-SceI[22][23] | H1
|
1VDE | Saccharomyces cerevisiae | E | 5' ATCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGGCA 3' TAGATACAGCCCACGCCTCTTTCTCCATTACTTTACCGT
|
5' ---ATCTATGTCGGGTGC GGAGAAAGAGGTAATGAAATGGCA--- 3' 3' ---TAGATACAGCC CACGCCTCTTTCTCCATTACTTTACCGT--- 5'
| |
I-SceII[24][25][26] | H1
|
Saccharomyces cerevisiae | E | mito | 5' TTTTGATTCTTTGGTCACCCTGAAGTATA 3' AAAACTAAGAAACCAGTGGGACTTCATAT
|
5' ---TTTTGATTCTTTGGTCACCC TGAAGTATA--- 3' 3' ---AAAACTAAGAAACCAG TGGGACTTCATAT--- 5'
| |
I-SecIII[24][27][28] | H1
|
Saccharomyces cerevisiae | E | mito | 5' ATTGGAGGTTTTGGTAACTATTTATTACC 3' TAACCTCCAAAACCATTGATAAATAATGG
|
5' ---ATTGGAGGTTTTGGTAAC TATTTATTACC--- 3' 3' ---TAACCTCCAAAACC ATTGATAAATAATGG--- 5'
| |
I-SceIV[24][29][30] | H1
|
Saccharomyces cerevisiae | E | mito | 5' TCTTTTCTCTTGATTAGCCCTAATCTACG 3' AGAAAAGAGAACTAATCGGGATTAGATGC
|
5' ---TCTTTTCTCTTGATTA GCCCTAATCTACG--- 3' 3' ---AGAAAAGAGAAC TAATCGGGATTAGATGC--- 5'
| |
I-SceV[24][31] | H3
|
Saccharomyces cerevisiae | E | mito | 5' AATAATTTTCTTCTTAGTAATGCC 3' TTATTAAAAGAAGAATCATTACGG
|
5' ---AATAATTTTCT TCTTAGTAATGCC--- 3' 3' ---TTATTAAAAGAAGAATCATTA CGG--- 5'
| |
I-SceVI[24][32] | H3
|
Saccharomyces cerevisiae | E | mito | 5' GTTATTTAATGTTTTAGTAGTTGG 3' CAATAAATTACAAAATCATCAACC
|
5' ---GTTATTTAATG TTTTAGTAGTTGG--- 3' 3' ---CAATAAATTACAAAATCATCA ACC--- 5'
| |
I-SceVII[20] | H1
|
Saccharomyces cerevisiae | E | mito | 5' TGTCACATTGAGGTGCACTAGTTATTAC 3' ACAGTGTAACTCCACGTGATCAATAATG
|
Unknown ** | |
I-Ssp6803I | H5
|
2OST | Synechocystis sp. PCC 6803 | B | 5' GTCGGGCTCATAACCCGAA 3' CAGCCCGAGTATTGGGCTT
|
5' ---GTCGGGCT CATAACCCGAA--- 3' 3' ---CAGCCCGAGTA TTGGGCTT--- 5'
| |
I-TevI[33][34][35] | H2
|
1I3J | Escherichia coli phage T4 | B | phage | 5' AGTGGTATCAACGCTCAGTAGATG 3' TCACCATAGT TGCGAGTCATCTAC
|
5' ---AGTGGTATCAAC GCTCAGTAGATG--- 3' 3' ---TCACCATAGT TGCGAGTCATCTAC--- 5'
|
I-TevII[33][36] | H2
|
Escherichia coli phage T4 | B | phage | 5' GCTTATGAGTATGAAGTGAACACGTTATTC 3' CGAATACTCATACTTCACTTGTGCAATAAG
|
5' ---GCTTATGAGTATGAAGTGAACACGT TATTC--- 3' 3' ---CGAATACTCATACTTCACTTGTG CAATAAG--- 5'
| |
I-TevIII[37] | H3
|
Escherichia coli phage RB3 | B | phage | 5' TATGTATCTTTTGCGTGTACCTTTAACTTC 3' ATACATAGAAAACGCACATGGAAATTGAAG
|
5' ---T ATGTATCTTTTGCGTGTACCTTTAACTTC--- 3' 3' ---AT ACATAGAAAACGCACATGGAAATTGAAG--- 5'
| |
PI-TliI[38][39] | H1
|
Thermococcus litoralis | A | chrm | 5' TAYGCNGAYACNGACGGYTTYT 3' ATRCGNCTRTGNCTGCCTAARA
|
5' ---TAYGCNGAYACNGACGG YTTYT--- 3' 3' ---ATRCGNCTRTGNC TGCCTAARA--- 5'
| |
PI-TliII[22][39][40] | H1
|
Thermococcus litoralis | A | chrm | 5' AAATTGCTTGCAAACAGCTATTACGGCTAT 3' TTTAACGAACGTTTGTCGATAATGCCGATA
|
Unknown ** | |
I-Tsp061I | H1
|
2DCH | Thermoproteus sp. IC-061 | A | 5' CTTCAGTATGCCCCGAAAC 3' GAAGTCATACGGGGCTTTG
|
5' ---CTTCAGTAT GCCCCGAAAC--- 3' 3' ---GAAGT CATACGGGGCTTTG--- 5'
| |
I-Vdi141I | H1
|
3E54 | Vulcanisaeta distributa IC-141 | A | 5' CCTGACTCTCTTAAGGTAGCCAAA 3' GGACTGAGAGAATTCCATCGGTTT
|
5' ---CCTGACTCTCTTAA GGTAGCCAAA--- 3' 3' ---GGACTGAG 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.