List of homing endonuclease cutting sites

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]

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: Homing endonuclease § Nomenclature.)
• 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: Homing endonuclease § Structural families.)
• 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	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.

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: Roberts RJ, Vincze T, Posfai J, Macelis D. "REBASE". Retrieved 2010-01-07. Restriction Enzyme Database.
• Database of inteins, hosted by New England Biolabs. Perler FB. "InBase". Archived from the original on 2010-08-02. Retrieved 2010-02-05. The Intein Database and Registry.[41]
• Detailed information for biochemical experiments: "Enzyme finder". Archived from the original on 2010-01-08. Retrieved 2010-01-07. New England Biolabs enzyme finder.
• Alphabetical list of enzymes and their restriction sites: "GenScript Restriction Enzyme webpage". Archived from the original on 2009-07-04. Retrieved 2010-01-07.
• General information about restriction sites and biochemical conditions for restriction reactions: "Restriction Enzymes Resource". Archived from the original on 2002-02-03. Retrieved 2010-01-07. Promega restriction enzymes webpage.

Databases of proteins:

• Database of protein structures, solved at atomic resolution: "PDB". Research Collaboratory for Structural Bioinformatics (RCSB). Archived from the original on 2015-04-07. Retrieved 2010-01-25. RCSB Protein Data Bank.
• Databases of proteins: Swiss Institute of Bioinformatics (SIB); European Bioinformatics Institute (EBI). "UniProtKB/Swiss-Prot & TrEMBL". Retrieved 2010-01-25. Swiss-Prot is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. TrEMBL is a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot.

Notes and references

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