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 acts on the own cellular DNA of the cell that synthesize them; to be precise, in the opposite allele of the gene that encode them.^[1]

Further information: Homing endonuclease.

1 Homing endonucleases
2 See also
3 Information sources
4 References

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: see the section "Nomenclature" in the article "Homing endonuclease".)
SF (Structural family): Any of the four established families for this kind of proteins, based in their shared structural motifs: HI: LAGLIDADG family – HII: GIY-YIG family – HIII: H-N-H family – HIV: His-Cys box family. (Further reading: see the section "Structural families" in the article "Homing endonuclease".)
PDB code: Code used to identify the structure of a protein in the PDB database.
Source: Organism that naturally produces the enzyme.
D: Biological domain of the source: A: archaea – B: bacteria – E: eukarya.
SCL: Subcelullar location: chloro: chloroplast – chrm: chromosomal – mito: mitochondrial – nuclear: extrachromosomal nuclear – 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]	`HI`	1P8K	Aspergillus nidulans	E	mito	`5' TTGAGGAGGTTTCTCTGTAAATAA` `3' AACTCCTCCAAAGAGACATTTATT`	`5' ---TTGAGGAGGTTTC TCTGTAAATAA--- 3'` `3' ---AACTCCTCC AAAGAGACATTTATT--- 5'`
I-CeuI ^[3]^[4]^[5]^[6]	`HI`	2EX5	Chlamydomonas eugametos	E	chloro	`5' TAACTATAACGGTCCTAAGGTAGCGA` `3' ATTGATATTGCCAGGATTCCATCGCT`	`5' ---TAACTATAACGGTCCTAA GGTAGCGA--- 3'` `3' ---ATTGATATTGCCAG GATTCCATCGCT--- 5'`
I-ChuI ^[7]^[8]	`HI`		Chlamydomonas humicola	E	chloro	`5' GAAGGTTTGGCACCTCGATGTCGGCTCATC` `3' CTTCCAAACCGTGGAGCTACAGCCGAGTAG`	`5' ---GAAGGTTTGGCACCTCG ATGTCGGCTCATC--- 3'` `3' ---CTTCCAAACCGTG GAGCTACAGCCGAGTAG--- 5'`
I-CpaI ^[8]^[9]	`HI`		Chlamydomonas pallidostigmata	E	chloro	`5' CGATCCTAAGGTAGCGAAATTCA` `3' GCTAGGATTCCATCGCTTTAAGT`	`5' ---CGATCCTAAGGTAGCGAA ATTCA--- 3'` `3' ---GCTAGGATTCCATC GCTTTAAGT--- 5'`
I-CpaII ^[10]	`HI`		Chlamydomonas pallidostigmata	E	chloro	`5' CCCGGCTAACTCTGTGCCAG` `3' GGGCCGATTGAGACACGGTC`	`5' ---CCCGGCTAACTC TGTGCCAG--- 3'` `5' ---GGGCCGAT TGAGACACGGTC--- 3'`
I-CreI ^[11]	`HI`	1BP7	Chlamydomonas reinhardtii	E	chloro	`5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG` `3' GACCCAAGTTTTGCAGCACTCTGTCAAACC`	`5' ---CTGGGTTCAAAACGTCGTGA GACAGTTTGG--- 3'` `3' ---GACCCAAGTTTTGCAG CACTCTGTCAAACC--- 5'`
I-DmoI	`HI`	1B24	Desulfurococcus mobilis	A	chrm	`5' ATGCCTTGCCGGGTAAGTTCCGGCGCGCAT` `3' TACGGAACGGCCCATTCAAGGCCGCGCGTA`	`5' ---ATGCCTTGCCGGGTAA GTTCCGGCGCGCAT--- 3'` `3' ---TACGGAACGGCC CATTCAAGGCCGCGCGTA--- 5'`
H-DreI ^[12]		1MOW	Escherichia coli pI-DreI	B		`5' CAAAACGTCGTAAGTTCCGGCGCG` `3' GTTTTGCAGCATTCAAGGCCGCGC`	`5' ---CAAAACGTCGTAA GTTCCGGCGCG--- 3'` `3' ---GTTTTGCAG CATTCAAGGCCGCGC--- 5'`
I-HmuI ^[13]^[14]	`HIII`	1U3E	Bacillus subtilis phage SPO1	B	phage	`5' AGTAATGAGCCTAACGCTCAGCAA` `3' TCATTACTCGGATTGCGAGTCGTT`	Nicking endonuclease: * `3' ---TCATTACTCGGATTGC GAGTCGTT--- 5'`
I-HmuII ^[14]^[15]	`HIII`		Bacillus subtilis phage SP82	B	phage	`5' AGTAATGAGCCTAACGCTCAACAA` `3' TCATTACTCGGATTGCGAGTTGTT`	Nicking endonuclease: * `3' ---TCATTACTCGGATTGCGAGTTGTTN₃₅ NNNN--- 5'`
I-LlaI ^[16]^[17]	`HIII`		Lactococcus lactis	B	chrm	`5' CACATCCATAACCATATCATTTTT` `3' GTGTAGGTATTGGTATAGTAAAAA`	`5' ---CACATCCATAA CCATATCATTTTT--- 3'` `3' ---GTGTAGGTATTGGTATAGTAA AAA--- 5'`
I-MsoI		1M5X	Monomastix sp.	E		`5' CTGGGTTCAAAACGTCGTGAGACAGTTTGG` `3' GACCCAAGTTTTGCAGCACTCTGTCAAACC`	`5' ---CTGGGTTCAAAACGTCGTGA GACAGTTTGG--- 3'` `3' ---GACCCAAGTTTTGCAG CACTCTGTCAAACC--- 5'`
PI-PfuI		1DQ3	Pyrococcus furiosus Vc1	A		`5' GAAGATGGGAGGAGGGACCGGACTCAACTT` `3' CTTCTACCCTCCTCCCTGGCCTGAGTTGAA`	`5' ---GAAGATGGGAGGAGGG ACCGGACTCAACTT--- 3'` `3' ---CTTCTACCCTCC TCCCTGGCCTGAGTTGAA--- 5'`
PI-PkoII		2CW7	Pyrococcus kodakaraensis KOD1	A		`5' CAGTACTACGGTTAC` `3' GTCATGATGCCAATG`	`5' ---CAGTACTACG GTTAC--- 3'` `3' ---GTCATG ATGCCAATG--- 5'`
I-PorI ^[18]^[19]	`HIII`		Pyrobaculum organotrophum	A	chrm	`5' GCGAGCCCGTAAGGGTGTGTACGGG` `3' CGCTCGGGCATTCCCACACATGCCC`	`5' ---GCGAGCCCGTAAGGGT GTGTACGGG--- 3'` `3' ---CGCTCGGGCATT CCCACACATGCCC--- 5'`
I-PpoI	`HIV`	1EVX	Physarum polycephalum	E	nuclear	`5' TAACTATGACTCTCTTAAGGTAGCCAAAT` `3' ATTGATACTGAGAGAATTCCATCGGTTTA`	`5' ---TAACTATGACTCTCTTAA GGTAGCCAAAT--- 3'` `3' ---ATTGATACTGAGAG AATTCCATCGGTTTA--- 5'`
PI-PspI	`HI`		Pyrococcus sp.	A	chrm	`5' TGGCAAACAGCTATTATGGGTATTATGGGT` `3' ACCGTTTGTCGATAATACCCATAATACCCA`	`5' ---TGGCAAACAGCTATTAT GGGTATTATGGGT--- 3'` `3' ---ACCGTTTGTCGAT AATACCCATAATACCCA--- 5'`
I-ScaI ^[20]^[21]	`HI`		Saccharomyces capensis	E	mito	`5' TGTCACATTGAGGTGCACTAGTTATTAC` `3' ACAGTGTAACTCCACGTGATCAATAATG`	`5' ---TGTCACATTGAGGTGCACT AGTTATTAC--- 3'` `3' ---ACAGTGTAACTCCAC GTGATCAATAATG--- 5'`
I-SceI ^[4]^[5]	`HI`	1R7M	Saccharomyces cerevisiae	E	mito	`5' AGTTACGCTAGGGATAACAGGGTAATATAG` `3' TCAATGCGATCCCTATTGTCCCATTATATC`	`5' ---AGTTACGCTAGGGATAA CAGGGTAATATAG--- 3'` `3' ---TCAATGCGATCCC TATTGTCCCATTATATC--- 5'`
PI-SceI ^[22]^[23]	`HI`	1VDE	Saccharomyces cerevisiae	E		`5' ATCTATGTCGGGTGCGGAGAAAGAGGTAATGAAATGGCA` `3' TAGATACAGCCCACGCCTCTTTCTCCATTACTTTACCGT`	`5' ---ATCTATGTCGGGTGC GGAGAAAGAGGTAATGAAATGGCA--- 3'` `3' ---TAGATACAGCC CACGCCTCTTTCTCCATTACTTTACCGT--- 5'`
I-SceII ^[24]^[25]^[26]	`HI`		Saccharomyces cerevisiae	E	mito	`5' TTTTGATTCTTTGGTCACCCTGAAGTATA` `3' AAAACTAAGAAACCAGTGGGACTTCATAT`	`5' ---TTTTGATTCTTTGGTCACCC TGAAGTATA--- 3'` `3' ---AAAACTAAGAAACCAG TGGGACTTCATAT--- 5'`
I-SecIII ^[24]^[27]^[28]	`HI`		Saccharomyces cerevisiae	E	mito	`5' ATTGGAGGTTTTGGTAACTATTTATTACC` `3' TAACCTCCAAAACCATTGATAAATAATGG`	`5' ---ATTGGAGGTTTTGGTAAC TATTTATTACC--- 3'` `3' ---TAACCTCCAAAACC ATTGATAAATAATGG--- 5'`
I-SceIV ^[24]^[29]^[30]	`HI`		Saccharomyces cerevisiae	E	mito	`5' TCTTTTCTCTTGATTAGCCCTAATCTACG` `3' AGAAAAGAGAACTAATCGGGATTAGATGC`	`5' ---TCTTTTCTCTTGATTA GCCCTAATCTACG--- 3'` `3' ---AGAAAAGAGAAC TAATCGGGATTAGATGC--- 5'`
I-SceV ^[24]^[31]	`HIII`		Saccharomyces cerevisiae	E	mito	`5' AATAATTTTCTTCTTAGTAATGCC` `3' TTATTAAAAGAAGAATCATTACGG`	`5' ---AATAATTTTCT TCTTAGTAATGCC--- 3'` `3' ---TTATTAAAAGAAGAATCATTA CGG--- 5'`
I-SceVI ^[24]^[32]	`HIII`		Saccharomyces cerevisiae	E	mito	`5' GTTATTTAATGTTTTAGTAGTTGG` `3' CAATAAATTACAAAATCATCAACC`	`5' ---GTTATTTAATG TTTTAGTAGTTGG--- 3'` `3' ---CAATAAATTACAAAATCATCA ACC--- 5'`
I-SceVII ^[20]	`HI`		Saccharomyces cerevisiae	E	mito	`5' TGTCACATTGAGGTGCACTAGTTATTAC` `3' ACAGTGTAACTCCACGTGATCAATAATG`	Unknown **
I-Ssp6803I		2OST	Synechocystis sp. PCC 6803	B		`5' GTCGGGCTCATAACCCGAA` `3' CAGCCCGAGTATTGGGCTT`	`5' ---GTCGGGCT CATAACCCGAA--- 3'` `3' ---CAGCCCGAGTA TTGGGCTT--- 5'`
I-TevI ^[33]^[34]^[35]	`HII`	1I3J	Escherichia coli phage T4	B	phage	`5' AGTGGTATCAACGCTCAGTAGATG` `3' TCACCATAGT TGCGAGTCATCTAC`	`5' ---AGTGGTATCAAC GCTCAGTAGATG--- 3'` `3' ---TCACCATAGT TGCGAGTCATCTAC--- 5'`
I-TevII ^[33]^[36]	`HII`		Escherichia coli phage T4	B	phage	`5' GCTTATGAGTATGAAGTGAACACGTTATTC` `3' CGAATACTCATACTTCACTTGTGCAATAAG`	`5' ---GCTTATGAGTATGAAGTGAACACGT TATTC--- 3'` `3' ---CGAATACTCATACTTCACTTGTG CAATAAG--- 5'`
I-TevIII ^[37]	`HIII`		Escherichia coli phage RB3	B	phage	`5' TATGTATCTTTTGCGTGTACCTTTAACTTC` `3' ATACATAGAAAACGCACATGGAAATTGAAG`	`5' ---T ATGTATCTTTTGCGTGTACCTTTAACTTC--- 3'` `3' ---AT ACATAGAAAACGCACATGGAAATTGAAG--- 5'`
PI-TliI ^[38]^[39]	`HI`		Thermococcus litoralis	A	chrm	`5' TAYGCNGAYACNGACGGYTTYT` `3' ATRCGNCTRTGNCTGCCTAARA`	`5' ---TAYGCNGAYACNGACGG YTTYT--- 3'` `3' ---ATRCGNCTRTGNC TGCCTAARA--- 5'`
PI-TliII ^[22]^[39]^[40]	`HI`		Thermococcus litoralis	A	chrm	`5' AAATTGCTTGCAAACAGCTATTACGGCTAT` `3' TTTAACGAACGTTTGTCGATAATGCCGATA`	Unknown **
I-Tsp061I		2DCH	Thermoproteus sp. IC-061	A		`5' CTTCAGTATGCCCCGAAAC` `3' GAAGTCATACGGGGCTTTG`	`5' ---CTTCAGTAT GCCCCGAAAC--- 3'` `3' ---GAAGT CATACGGGGCTTTG--- 5'`
I-Vdi141I		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.

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". http://rebase.neb.com. Retrieved 2010-01-07. "Restriction Enzyme Database."
Database of inteins, hosted by New England Biolabs©. Perler FB. "InBase". http://www.neb.com/neb/inteins.html. Retrieved 2010-02-05. "The Intein Database and Registry" ^[41].
Detailed information for biochemical experiments: "Enzyme finder". http://www.neb.com/nebecomm/EnzymeFinder.asp?. Retrieved 2010-01-07. "New England Biolabs© enzyme finder."
Alphabetical list of enzymes and their restriction sites: "GenScript© Restriction Enzyme webpage". http://www.genscript.com/cgi-bin/products/enzyme.cgi?op=all_ez. Retrieved 2010-01-07.
General information about restriction sites and biochemical conditions for restriction reactions: "Restriction Enzymes Resource". http://www.promega.com/guides/re_guide/. 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). http://www.pdb.org. Retrieved 2010-01-25. "RCSB Protein Data Bank."
Databases of proteins: Swiss Institute of Bioinformatics (SIB) & European Bioinformatics Institute (EBI). "UniProtKB/Swiss-Prot & TrEMBL". http://www.expasy.ch/sprot. 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 a computer-annotated supplement of Swiss-Prot that contains all the translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot."

References

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List of homing endonuclease cutting sites

Contents

Homing endonucleases

See also

Information sources

References