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.

Homing endonucleases The list includes some of the most studied examples. The following concepts have been detailed: Enzyme: Accepted name of the molecule, according to the internationally adopted nomenclature. Bibliographical references. (Further reading: .) SF (structural family): Any of the established families for this kind of proteins, based in their shared structural motifs: 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: .) PDB code: Code used to identify the structure of a protein in the PDB database. If no structure is available, a UniProt identifier is given instead. Source: Organism that naturally produces the enzyme. D: Biological domain of the source: A: archaea – B: bacteria – E: eukarya. SCL: Subcellular genome: chloro: chloroplast – chrm: chromosomal – mito: mitochondrial – plasmid: other extrachromosomal – phage: bacteriophage. Recognition sequence: Sequence of DNA recognized by the enzyme. The enzyme is specifically bound to this sequence. Cut: Cutting site and products of the cut. Both the recognition sequence and the cutting site match usually, but sometimes the cutting site can be dozens of nucleotides away from the recognition site.

Enzyme SF PDB code Source D SCL Recognition sequence CutI-AniI H1 Aspergillus nidulans E mito 5' TTGAGGAGGTTTCTCTGTAAATAA 3' AACTCCTCCAAAGAGACATTTATT 5' ---TTGAGGAGGTTTC TCTGTAAATAA--- 3' 3' ---AACTCCTCC AAAGAGACATTTATT--- 5' I-CeuI H1 Chlamydomonas eugametos E chloro 5' TAACTATAACGGTCCTAAGGTAGCGA 3' ATTGATATTGCCAGGATTCCATCGCT 5' ---TAACTATAACGGTCCTAA GGTAGCGA--- 3' 3' ---ATTGATATTGCCAG GATTCCATCGCT--- 5' I-ChuI H1 Chlamydomonas humicola E chloro 5' GAAGGTTTGGCACCTCGATGTCGGCTCATC 3' CTTCCAAACCGTGGAGCTACAGCCGAGTAG 5' ---GAAGGTTTGGCACCTCG ATGTCGGCTCATC--- 3' 3' ---CTTCCAAACCGTG GAGCTACAGCCGAGTAG--- 5' I-CpaI H1 Chlamydomonas pallidostigmata E chloro 5' CGATCCTAAGGTAGCGAAATTCA 3' GCTAGGATTCCATCGCTTTAAGT 5' ---CGATCCTAAGGTAGCGAA ATTCA--- 3' 3' ---GCTAGGATTCCATC GCTTTAAGT--- 5' I-CpaII H1 Chlamydomonas pallidostigmata E chloro 5' CCCGGCTAACTCTGTGCCAG 3' GGGCCGATTGAGACACGGTC 5' ---CCCGGCTAACTC TGTGCCAG--- 3' 5' ---GGGCCGAT TGAGACACGGTC--- 3'I-CreI H1 Chlamydomonas reinhardtii E chloro 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG 3' GACCCAAGTTTTGCAGCACTCTGTCAAACC 5' ---CTGGGTTCAAAACGTCGTGA GACAGTTTGG--- 3' 3' ---GACCCAAGTTTTGCAG CACTCTGTCAAACC--- 5' I-DmoI H1 Desulfurococcus mobilis A chrm 5' ATGCCTTGCCGGGTAAGTTCCGGCGCGCAT 3' TACGGAACGGCCCATTCAAGGCCGCGCGTA 5' ---ATGCCTTGCCGGGTAA GTTCCGGCGCGCAT--- 3' 3' ---TACGGAACGGCC CATTCAAGGCCGCGCGTA--- 5' H-DreI H1 Hybrid: I-DmoI and I-CreI AE 5' CAAAACGTCGTAAGTTCCGGCGCG 3' GTTTTGCAGCATTCAAGGCCGCGC 5' ---CAAAACGTCGTAA GTTCCGGCGCG--- 3' 3' ---GTTTTGCAG CATTCAAGGCCGCGC--- 5' I-HmuIH3 Bacillus subtilis phage SP01 B phage 5' AGTAATGAGCCTAACGCTCAGCAA 3' TCATTACTCGGATTGCGAGTCGTT Nicking endonuclease: * 3' ---TCATTACTCGGATTGC GAGTCGTT--- 5' I-HmuIIH3 Bacillus subtilis phage SP82 B phage 5' AGTAATGAGCCTAACGCTCAACAA 3' TCATTACTCGGATTGCGAGTTGTT Nicking endonuclease: * 3' ---TCATTACTCGGATTGCGAGTTGTTN35 NNNN--- 5' I-LlaIH3 Lactococcus lactis B chrm 5' CACATCCATAACCATATCATTTTT 3' GTGTAGGTATTGGTATAGTAAAAA 5' ---CACATCCATAA CCATATCATTTTT--- 3' 3' ---GTGTAGGTATTGGTATAGTAA AAA--- 5' I-MsoI H1 Monomastix sp. E 5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG 3' GACCCAAGTTTTGCAGCACTCTGTCAAACC 5' ---CTGGGTTCAAAACGTCGTGA GACAGTTTGG--- 3' 3' ---GACCCAAGTTTTGCAG CACTCTGTCAAACC--- 5' PI-PfuI H1 Pyrococcus furiosus Vc1 A 5' GAAGATGGGAGGAGGGACCGGACTCAACTT 3' CTTCTACCCTCCTCCCTGGCCTGAGTTGAA 5' ---GAAGATGGGAGGAGGG ACCGGACTCAACTT--- 3' 3' ---CTTCTACCCTCC TCCCTGGCCTGAGTTGAA--- 5' PI-PkoII H1 Pyrococcus kodakarensis BAA-918 A 5' CAGTACTACGGTTAC 3' GTCATGATGCCAATG 5' ---CAGTACTACG GTTAC--- 3' 3' ---GTCATG ATGCCAATG--- 5' I-PorIH3 Pyrobaculum organotrophum A chrm 5' GCGAGCCCGTAAGGGTGTGTACGGG 3' CGCTCGGGCATTCCCACACATGCCC 5' ---GCGAGCCCGTAAGGGT GTGTACGGG--- 3' 3' ---CGCTCGGGCATT CCCACACATGCCC--- 5' I-PpoI H4 Physarum polycephalum E plasmid 5' TAACTATGACTCTCTTAAGGTAGCCAAAT 3' ATTGATACTGAGAGAATTCCATCGGTTTA 5' ---TAACTATGACTCTCTTAA GGTAGCCAAAT--- 3' 3' ---ATTGATACTGAGAG AATTCCATCGGTTTA--- 5' PI-PspI H1 Pyrococcus sp. A chrm 5' TGGCAAACAGCTATTATGGGTATTATGGGT 3' ACCGTTTGTCGATAATACCCATAATACCCA 5' ---TGGCAAACAGCTATTAT GGGTATTATGGGT--- 3' 3' ---ACCGTTTGTCGAT AATACCCATAATACCCA--- 5' I-ScaIH1 Saccharomyces capensis E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC 3' ACAGTGTAACTCCACGTGATCAATAATG 5' ---TGTCACATTGAGGTGCACT AGTTATTAC--- 3' 3' ---ACAGTGTAACTCCAC GTGATCAATAATG--- 5' I-SceI H1 Saccharomyces cerevisiae E mito 5' AGTTACGCTAGGGATAACAGGGTAATATAG 3' TCAATGCGATCCCTATTGTCCCATTATATC 5' ---AGTTACGCTAGGGATAA CAGGGTAATATAG--- 3' 3' ---TCAATGCGATCCC TATTGTCCCATTATATC--- 5' PI-SceI H1 Saccharomyces cerevisiae E 5' ATCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGGCA 3' TAGATACAGCCCACGCCTCTTTCTCCATTACTTTACCGT 5' ---ATCTATGTCGGGTGC GGAGAAAGAGGTAATGAAATGGCA--- 3' 3' ---TAGATACAGCC CACGCCTCTTTCTCCATTACTTTACCGT--- 5' I-SceII H1 Saccharomyces cerevisiae E mito 5' TTTTGATTCTTTGGTCACCCTGAAGTATA 3' AAAACTAAGAAACCAGTGGGACTTCATAT 5' ---TTTTGATTCTTTGGTCACCC TGAAGTATA--- 3' 3' ---AAAACTAAGAAACCAG TGGGACTTCATAT--- 5' I-SecIII H1 Saccharomyces cerevisiae E mito 5' ATTGGAGGTTTTGGTAACTATTTATTACC 3' TAACCTCCAAAACCATTGATAAATAATGG 5' ---ATTGGAGGTTTTGGTAAC TATTTATTACC--- 3' 3' ---TAACCTCCAAAACC ATTGATAAATAATGG--- 5' I-SceIV H1 Saccharomyces cerevisiae E mito 5' TCTTTTCTCTTGATTAGCCCTAATCTACG 3' AGAAAAGAGAACTAATCGGGATTAGATGC 5' ---TCTTTTCTCTTGATTA GCCCTAATCTACG--- 3' 3' ---AGAAAAGAGAAC TAATCGGGATTAGATGC--- 5' I-SceV H3 Saccharomyces cerevisiae E mito 5' AATAATTTTCTTCTTAGTAATGCC 3' TTATTAAAAGAAGAATCATTACGG 5' ---AATAATTTTCT TCTTAGTAATGCC--- 3' 3' ---TTATTAAAAGAAGAATCATTA CGG--- 5' I-SceVI H3 Saccharomyces cerevisiae E mito 5' GTTATTTAATGTTTTAGTAGTTGG 3' CAATAAATTACAAAATCATCAACC 5' ---GTTATTTAATG TTTTAGTAGTTGG--- 3' 3' ---CAATAAATTACAAAATCATCA ACC--- 5' I-SceVII H1 Saccharomyces cerevisiae E mito 5' TGTCACATTGAGGTGCACTAGTTATTAC 3' ACAGTGTAACTCCACGTGATCAATAATG Unknown **I-Ssp6803IH5 Synechocystis sp. PCC 6803 B 5' GTCGGGCTCATAACCCGAA 3' CAGCCCGAGTATTGGGCTT 5' ---GTCGGGCT CATAACCCGAA--- 3' 3' ---CAGCCCGAGTA TTGGGCTT--- 5' I-TevI H2 Escherichia coli phage T4 B phage 5' AGTGGTATCAACGCTCAGTAGATG 3' TCACCATAGT TGCGAGTCATCTAC 5' ---AGTGGTATCAAC GCTCAGTAGATG--- 3' 3' ---TCACCATAGT TGCGAGTCATCTAC--- 5' I-TevII H2 Escherichia coli phage T4 B phage 5' GCTTATGAGTATGAAGTGAACACGTTATTC 3' CGAATACTCATACTTCACTTGTGCAATAAG 5' ---GCTTATGAGTATGAAGTGAACACGT TATTC--- 3' 3' ---CGAATACTCATACTTCACTTGTG CAATAAG--- 5' I-TevIII H3 Escherichia coli phage RB3 B phage 5' TATGTATCTTTTGCGTGTACCTTTAACTTC 3' ATACATAGAAAACGCACATGGAAATTGAAG 5' ---T ATGTATCTTTTGCGTGTACCTTTAACTTC--- 3' 3' ---AT ACATAGAAAACGCACATGGAAATTGAAG--- 5' PI-TliI H1 Thermococcus litoralis A chrm 5' TAYGCNGAYACNGACGGYTTYT 3' ATRCGNCTRTGNCTGCCTAARA 5' ---TAYGCNGAYACNGACGG YTTYT--- 3' 3' ---ATRCGNCTRTGNC TGCCTAARA--- 5' PI-TliII H1 Thermococcus litoralis A chrm 5' AAATTGCTTGCAAACAGCTATTACGGCTAT 3' TTTAACGAACGTTTGTCGATAATGCCGATA Unknown **I-Tsp061I H1 Thermoproteus sp. IC-061 A 5' CTTCAGTATGCCCCGAAAC 3' GAAGTCATACGGGGCTTTG 5' ---CTTCAGTAT GCCCCGAAAC--- 3' 3' ---GAAGT CATACGGGGCTTTG--- 5' I-Vdi141I H1 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.

See also List of restriction enzyme cutting sites. Homing endonuclease. Restriction enzyme. Introns and inteins. Intragenomic conflict: Homing endonuclease genes. I-CreI homing endonuclease. Isoschizomer. Detailed articles about certain restriction enzymes: EcoRI, HindIII, BglII.

Information sources Databases and lists of restriction enzymes: Very comprehensive database of restriction enzymes supported by New England Biolabs. It includes all kind of biological, structural, kinetical and commercial information about thousands of enzymes. Also includes related literature for every molecule: Database of inteins, hosted by New England Biolabs. . Detailed information for biochemical experiments: Alphabetical list of enzymes and their restriction sites: General information about restriction sites and biochemical conditions for restriction reactions: Databases of proteins: Database of protein structures, solved at atomic resolution: Databases of proteins:

Notes and references