List of restriction enzyme cutting sites
A restriction enzyme or restriction endonuclease is a special type of biological macromolecule that functions as part of the "immune system" in bacteria. One special kind of restriction enzymes is the class of "homing endonucleases", these being present in all three domains of life, although their function seems to be very different from one domain to another.
The classical restriction enzymes cut up and hence render harmless any unknown (non-cellular) DNA that enters a bacterial cell as a result of a viral infection. They recognize a specific DNA sequence, usually short (3 to 8 bp), and cut it, producing either blunt or overhung ends, either at or nearby the recognition site.
Restriction enzymes are very variable. An organism often has several different enzymes, each specific to a distinct DNA sequence.
Restriction enzymes catalog
The list includes some of the most studied examples of restriction endoncleases. The following information is given:
- Enzyme: Accepted name of the molecule, according to the internationally adopted nomenclature, and bibliographical references. (Further reading: see the section "Nomenclature" in the article "Restriction enzyme".)
- PDB code: Code used to identify the structure of a protein in the PDB database of protein structures. The 3D atomic structure of a protein provides highly valuable information to understand the intimate details of its mechanism of action.
- Source: Organism that naturally produces the enzyme.
- Recognition sequence: Sequence of DNA recognized by the enzyme and to which it specifically binds.
- Cut: Cutting site and DNA products of the cut. The recognition sequence and the cutting site usually match, but sometimes the cutting site can be dozens of nucleotides away from the recognition site.
- Isoschizomers and neoschizomers: An isoschizomer is an enzyme that recognizes the same sequence as another. A neoschizomer is a special type of isoschizomer that recognizes the same sequence as another, but cuts in a different manner. A maximum number of 8-10 most common isoschizomers are indicated for every enzyme but there may be many more. Neoschizomers are shown in bold and green color font (e.g.: BamHI). When "None on date" is indicated, that means that there were no registered isoschizomers in the databases on that date with a clearly defined cutting site. Isoschizomers indicated in white font and grey background correspond to enzymes not listed in the current lists:
as in this not listed enzyme: EcoR70I
The whole list contains more than 1,200 enzymes, but databases register about 4,000.
To make an accessible navigation the list has been divided in different pages and sections. Choose a letter in the next table of contents:
Notes and references
- Roberts RJ (January 1980). "Restriction and modification enzymes and their recognition sequences". Nucleic Acids Res. 8 (1): r63–r80. doi:10.1093/nar/8.1.197-d. PMC 327257. PMID 6243774.
- Smith HO, Nathans D (December 1973). "Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes". J. Mol. Biol. 81 (3): 419–23. doi:10.1016/0022-2836(73)90152-6. PMID 4588280.
- Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SKh, Dryden DT, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Krüger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, Nagaraja V, Piekarowicz A, Pingoud A, Raleigh E, Rao DN, Reich N, Repin VE, Selker EU, Shaw PC, Stein DC, Stoddard BL, Szybalski W, Trautner TA, Van Etten JL, Vitor JM, Wilson GG, Xu SY (April 2003). "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes". Nucleic Acids Res. 31 (7): 1805–12. doi:10.1093/nar/gkg274. PMC 152790. PMID 12654995.
- Jeremy M. Berg, John L. Tymoczko, Lubert Stryer; Web content by Neil D. Clarke (2002). "3. Protein Structure and Function". Biochemistry. San Francisco: W. H. Freeman. ISBN 0-7167-4684-0.
- Anfinsen C.B. (1973). "Principles that Govern the Folding of Protein Chains". Science 181 (4096): 223–30. doi:10.1126/science.181.4096.223. PMID 4124164.
- Kessler C, Manta V (August 1990). "Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3)". Gene 92 (1-2): 1–248. doi:10.1016/0378-1119(90)90486-B. PMID 2172084.
- Pingoud A, Jeltsch A (September 2001). "Structure and function of type II restriction endonucleases". Nucleic Acids Res. 29 (18): 3705–27. doi:10.1093/nar/29.18.3705. PMC 55916. PMID 11557805.
- Roberts RJ, Vincze T, Posfai, J, Macelis D. "REBASE". Retrieved 2010-05-23.
Restriction Enzyme Database.
- List of homing endonuclease cutting sites
- Restriction enzyme.
- Detailed articles about certain restriction enzymes: EcoRI, HindIII, BglII.
- Homing endonuclease.
- Introns and inteins.
- Intragenomic conflict: Homing endonuclease genes.
- I-CreI homing endonuclease.
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 2010-05-23.
Restriction Enzyme Database.
- Detailed information for biochemical experiments: "Enzyme finder". Retrieved 2010-01-07.
New England Biolabs© enzyme finder.
- Alphabetical list of enzymes and their restriction sites: "GenScript© Restriction Enzyme webpage". Retrieved 2010-01-07.
- General information about restriction sites and biochemical conditions for restriction reactions: "Restriction Enzymes Resource". Retrieved 2010-01-07.
Promega© restriction enzymes webpage.
Databases of proteins:
- Database of structures of proteins, solved at atomic resolution: "PDB". Retrieved 2010-01-25.
Worldwide 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.