restriction enzyme: Definition from Answers.com

Restriction enzymes are bacterial proteins that recognize specific DNA sequences and cut DNA at or near the recognition site. These enzymes are widely used in molecular genetics for analyzing DNA and creating recombinant DNA molecules.

Biological Function and Historical Background

Restriction enzymes apparently evolved as a primitive immune system in bacteria. If viruses enter a bacterial cell containing restriction enzymes, the viral DNA is fragmented. Destruction of the viral DNA prevents destruction of the bacterial cell by the virus. The term "restriction" derives from the phenomenon in which bacterial viruses are restricted from replicating in certain strains of bacteria by enzymes that cleave the viral DNA, but leave the bacterial DNA untouched. In bacteria, restriction enzymes form a system with modification enzymes that methylate the bacterial DNA. Methylation of DNA at the recognition sequence typically protects the microbe from cleaving its own DNA.

Since the 1970s, restriction enzymes have had a very important role in recombinant DNA techniques, in both the creation and analysis of recombinant DNA molecules. The first restriction enzyme was isolated and characterized in 1968, and over 3,400 restriction enzymes have been discovered since. Of these enzymes, over 540 are currently commercially available.

Nomenclature and Classification

Restriction enzymes are named based on the organism in which they were discovered. For example, the enzyme Hind III was isolated from Haemophilus influenzae, strain Rd. The first three letters of the name are italicized because they abbreviate the genus and species names of the organism. The fourth letter typically comes from the bacterial strain designation. The Roman numerals are used to identify specific enzymes from bacteria that contain multiple restriction enzymes. Typically, the Roman numeral indicates the order in which restriction enzymes were discovered in a particular strain.

There are three classes of restriction enzymes, labeled types I, II, and III. Type I restriction systems consist of a single enzyme that performs both modification (methylation) and restriction activities. These enzymes recognize specific DNA sequences, but cleave the DNA strand randomly, at least 1,000 base pairs (bp) away from the recognition site. Type III restriction systems have separate enzymes for restriction and methylation, but these enzymes share a common subunit. These enzymes recognize specific DNA sequences, but cleave DNA at random sequences approximately twenty-five bp from the recognition sequence. Neither type I nor type III restriction systems have found much application in recombinant DNA techniques.

Type II restriction enzymes, in contrast, are heavily used in recombinant DNA techniques. Type II enzymes consist of single, separate proteins for restriction and modification. One enzyme recognizes and cuts DNA, the other enzyme recognizes and methylates the DNA. Type II restriction enzymes cleave the DNA sequence at the same site at which they recognize it. The only exception are type IIs (shifted) restriction enzymes, which cleave DNA on one side of the recognition sequence, within twenty nucleotides of the recognition site. Type II restriction enzymes discovered to date collectively recognize over 200 different DNA sequences.

Type II restriction enzymes can cleave DNA in one of three possible ways. In one case, these enzymes cleave both DNA strands in the middle of a recognition sequence, generating blunt ends. For example: (The notations 5′ and 3′ are used to indicate the orientation of a DNA molecule. The numbers 5 and 3 refer to specific carbon atoms in the deoxyribose sugar in DNA.)

These blunt ended fragments can be joined to any other DNA fragment with blunt ends, making these enzymes useful for certain types of DNA cloning experiments.

Type II restriction enzymes can also cleave DNA to leave a 3′ ("three prime") overhang. (An overhang means that the restriction enzyme leaves a short single-stranded "tail" of DNA at the site where the DNA was cut.) These 3′ overhanging ends can only join to another compatible 3′ overhanging end (that is, an end with the same sequence in the overhang). Finally, some type II enzymes can generate 5′ overhanging DNA ends, which can only be joined to a compatible 5′ end.

In the type II restriction enzymes discovered to date, the recognition sequences range from 4 bp to 9 bp long. Cleavage will not occur unless the full length of the recognition sequence is encountered. Enzymes with a short recognition sequence cut DNA frequently; restriction enzymes with 8 or 9 bp sequences typically cut DNA very infrequently, because these longer sequences are less common in the target DNA.

Use of Restriction Enzymes in Biotechnology

The ability of restriction enzymes to reproducibly cut DNA at specific sequences has led to the widespread use of these tools in many molecular genetics techniques. Restriction enzymes can be used to map DNA fragments or genomes. Mapping means determining the order of the restriction enzyme sites in the genome. These maps form a foundation for much other genetic analysis. Restriction enzymes are also frequently used to verify the identity of a specific DNA fragment, based on the known restriction enzyme sites that it contains.

Perhaps the most important use of restriction enzymes has been in the generation of recombinant DNA molecules, which are DNAs that consist of genes or DNA fragments from two different organisms. Typically, bacterial DNA in the form of a plasmid (a small, circular DNA molecule) is joined to another piece of DNA (a gene) from another organism of interest. Restriction enzymes are used at several points in this process. They are used to digest the DNA from the experimental organism, in order to prepare the DNA for cloning. Then a bacterial plasmid or bacterial virus is digested with an enzyme that yields compatible ends. These compatible ends could be blunt (no overhang), or have complementary overhanging sequences. DNA from the experimental organism is mixed with DNA from the plasmid or virus, and the DNAs are joined with an enzyme called DNA ligase. As noted above, the identity of the recombinant DNA molecule is often verified by restriction enzyme digestion.

Restriction enzymes also have applications in several methods for identifying individuals or strains of a particular species. Pulsed field gel electrophoresis is a technique for separating large DNA fragments, typically fragments resulting from digesting a bacterial genome with a rare-cutting restriction enzyme. The reproducible pattern of DNA bands that is produced can be used to distinguish different strains of bacteria, and help pinpoint if a particular strain was the cause of a widespread disease outbreak, for example.

Restriction fragment length polymorphism (RFLP) analysis has been widely used for identification of individuals (humans and other species). In this technique, genomic DNA is isolated, digested with a restriction enzyme, separated by size in an agarose gel, then transferred to a membrane. The digested DNA on the membrane is allowed to bind to a radioactively or fluorescently labeled probe that targets specific sequences that are bracketed by restriction enzyme sites. The size of these fragments varies in different individuals, generating a "biological bar code" of restriction enzyme-digested DNA fragments, a pattern that is unique to each individual.

Restriction enzymes are likely to remain an important tool in modern genetics. The reproducibility of restriction enzyme digestion has made these enzymes critical components of many important recombinant DNA techniques.

Bibliography

Bloom, Mark V., Greg A. Freyer, and David A. Micklos. Laboratory DNA Science: An Introduction to Recombinant DNA Techniques and Methods of Genome Analysis. Menlo Park, CA: Addison-Wesley, 1996.

Cooper, Geoffrey. The Cell: A Molecular Approach. Washington, DC: ASM Press, 1997.

Kreuzer, Helen, and Adrianne Massey. Recombinant DNA and Biotechnology, 2nd ed. Washington, DC: ASM Press, 2000.

Lodish, Harvey, et al. Molecular Cell Biology, 4th ed. New York: W. H. Freeman, 2000.

Old, R. W., and S. B. Primrose. Principles of Gene Manipulation, 5th ed. London: Blackwell Scientific Publications, 1994.

Internet Resource

Roberts, Richard J., and Dana Macelis. Rebase.http://rebase.neb.com.

—Patrick G. Guilfoile

Restriction Enzyme Glossary

Restriction

The cutting of DNA at specific boundaries

Enzyme

A protein that catalyzes a chemical reaction

Molecular recognition

Used by restriction enzymes to locate specific sequences of DNA on which to bind and subsequently cleave

Recognition sequence

The DNA sequence to which restriction enzymes bind

Restriction site

The DNA sequence that is cleaved by the restriction enzyme

A Restriction Enzyme (or restriction endonuclease) is an enzyme that cuts DNA at specific recognition nucleotide sequences (with Type II restriction enzymes cutting Double stranded DNA) known as restriction sites.^[1]^[2]^[3] Such enzymes, found in bacteria and archaea, are thought to have evolved to provide a defense mechanism against invading viruses.^[4]^[5] Inside a bacterial host, the restriction enzymes selectively cut up foreign DNA in a process called restriction; host DNA is methylated by a modification enzyme (a methylase) to protect it from the restriction enzyme’s activity. Collectively, these two processes form the restriction modification system.^[6] To cut the DNA, a restriction enzyme makes two incisions, once through each sugar-phosphate backbone (i.e. each strand) of the DNA double helix.

Over 3000 restriction enzymes have been studied in detail, and more than 600 of these are available commercially^[7] and are routinely used for DNA modification and manipulation in laboratories.^[8]^[9]^[10]

Contents

1 History
2 Recognition site
3 Types
4 Nomenclature
5 Applications
6 Examples
7 See also
8 References
9 External links

History

For the first isolation of a restriction enzyme, HindII, in 1970,^[11]^[12] and the subsequent discovery and characterization of numerous restriction endonucleases,^[13] the 1978 Nobel Prize for Physiology or Medicine was awarded to Daniel Nathans, Werner Arber, and Hamilton O. Smith.^[14] Their discovery led to the development of recombinant DNA technology that allowed, for example, the large scale production of human insulin for diabetics using E. coli bacteria.^[15]

Recognition site

A palindromic recognition site reads the same on the reverse strand as it does on the forward strand when both are read in the same orientation

Restriction enzymes recognize a specific sequence of nucleotides^[2] and produce a double-stranded cut in the DNA. While recognition sequences vary between 4 and 8 nucleotides, many of them are palindromic, which correspond to nitrogenous base sequences that read the same backwards and forwards.^[16] In theory, there are two types of palindromic sequences that can be possible in DNA. The mirror-like palindrome is similar to those found in ordinary text, in which a sequence reads the same forward and backwards on a single strand of DNA strand, as in GTAATG. The inverted repeat palindrome is also a sequence that reads the same forward and backwards, but the forward and backward sequences are found in complementary DNA strands (i.e., of double-stranded DNA), as in GTATAC (GTATAC being complementary to CATATG).^[17] Inverted repeat palindromes are more common and have greater biological importance than mirror-like palindromes.

EcoRI digestion produces "sticky" ends,

whereas SmaI restriction enzyme cleavage produces "blunt" ends:

Recognition sequences in DNA differ for each restriction enzyme, producing differences in the length, sequence and strand orientation (5' end or the 3' end) of a sticky-end "overhang" of an enzyme restriction.^[18]

Different restriction enzymes that recognize the same sequence are known as neoschizomers. These often cleave in different locales of the sequence. Different enzymes that recognize and cleave in the same location are known as isoschizomers.

Types

Naturally occurring restriction endonucleases are categorized into four groups (Types I, II III, and IV) based on their composition and enzyme cofactor requirements, the nature of their target sequence, and the position of their DNA cleavage site relative to the target sequence.^[19]^[20]^[21] All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements,^[22]^[23] as summarised below:

Type I enzymes (EC 3.1.21.3) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (EC 2.1.1.72) activities.
Type II enzymes (EC 3.1.21.4) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase.
Type III enzymes (EC 3.1.21.5) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exist as part of a complex with a modification methylase (EC 2.1.1.72).
Type IV enzymes target normal DNA.

Type I

Type I restriction enzymes were the first to be identified and were first identified in two different strains (K-12 and B) of E. coli.^[24] These enzymes cut at a site that differs, and is a random distance (at least 1000 bp) away, from their recognition site. Cleavage at these random sites follows a process of DNA translocation, which shows that these enzymes are also molecular motors. The recognition site is asymmetrical and is composed of two specific portions—one containing 3–4 nucleotides, and another containing 4–5 nucleotides—separated by a non-specific spacer of about 6–8 nucleotides. These enzymes are multifunctional and are capable of both restriction and modification activities, depending upon the methylation status of the target DNA. The cofactors S-Adenosyl methionine (AdoMet), hydrolyzed adenosine triphosphate (ATP), and magnesium (Mg²⁺) ions, are required for their full activity. Type I restriction enzymes possess three subunits called HsdR, HsdM, and HsdS; HsdR is required for restriction; HsdM is necessary for adding methyl groups to host DNA (methyltransferase activity) and HsdS is important for specificity of the recognition (DNA-binding) site in addition to both restriction (DNA cleavage) and modification (DNA methyltransferase) activity.^[19]^[24]

Type II

Type II site-specific deoxyribonuclease

Structure of the homodimeric restriction enzyme EcoRI (cyan and green cartoon diagram) bound to double stranded DNA (brown tubes).^[25] Two catalytic manganese ions (one from each monomer) are shown as magenta spheres and are adjacent to the cleaved sites in the DNA made by the enzyme (depicted as gaps in the DNA backbone).

Identifiers

Databases

PDB structures

AmiGO / EGO

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PMC	articles
PubMed	articles

Typical type II restriction enzymes differ from type I restriction enzymes in several ways. They are a dimer of only one type of subunit; their recognition sites are usually undivided and palindromic and 4–8 nucleotides in length, they recognize and cleave DNA at the same site, and they do not use ATP or AdoMet for their activity—they usually require only Mg²⁺ as a cofactor.^[16] These are the most commonly available and used restriction enzymes. In the 1990s and early 2000s, new enzymes from this family were discovered that did not follow all the classical criteria of this enzyme class, and new subfamily nomenclature was developed to divide this large family into subcategories based on deviations from typical characteristics of type II enzymes.^[16] These subgroups are defined using a letter suffix.

Type IIB restriction enzymes (e.g. BcgI and BplI) are multimers, containing more than one subunit.^[16] They cleave DNA on both sides of their recognition to cut out the recognition site. They require both AdoMet and Mg²⁺ cofactors. Type IIE restriction endonucleases (e.g. NaeI) cleave DNA following interaction with two copies of their recognition sequence.^[16] One recognition site acts as the target for cleavage, while the other acts as an allosteric effector that speeds up or improves the efficiency of enzyme cleavage. Similar to type IIE enzymes, type IIF restriction endonucleases (e.g. NgoMIV) interact with two copies of their recognition sequence but cleave both sequences at the same time.^[16] Type IIG restriction endonucleases (Eco57I) do have a single subunit, like classical Type II restriction enzymes, but require the cofactor AdoMet to be active.^[16] Type IIM restriction endonucleases, such as DpnI, are able to recognize and cut methylated DNA.^[16] Type IIS restriction endonucleases (e.g. FokI) cleave DNA at a defined distance from their non-palindromic asymmetric recognition sites.^[16] These enzymes may function as dimers. Similarly, Type IIT restriction enzymes (e.g., Bpu10I and BslI) are composed of two different subunits. Some recognize palindromic sequences while others have asymmetric recognition sites.^[16]

Type III

Type III restriction enzymes (e.g. EcoP15) recognize two separate non-palindromic sequences that are inversely oriented. They cut DNA about 20-30 base pairs after the recognition site.^[26] These enzymes contain more than one subunit and require AdoMet and ATP cofactors for their roles in DNA methylation and restriction, respectively.^[27] They are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F).^[28]^[29]

Artificial Restriction Enzymes

Artificial restriction enzymes can be generated by fusing a natural or engineered DNA binding domain to a nuclease domain (often the cleavage domain of the type IIS restriction enzyme FokI^[30]). Such artificial restriction enzymes can target large DNA sites (up to 36 bp) and can be engineered to bind to desired DNA sequences.^[31] Zinc finger nucleases are the most commonly used artificial restriction enzymes and are generally used in genetic engineering applications,^[32]^[33]^[34]^[35] but can also be used for more standard gene cloning applications.^[36] Other artificial restriction enzymes are based on the DNA binding domain of TAL effectors.^[37]^[38]

Nomenclature

Derivation of the EcoRI name
Abbreviation	Meaning	Description
E	Escherichia	genus
co	coli	species
R	RY13	strain
I	First identified	order of identification in the bacterium

Since their discovery in the 1970s, more than 100 different restriction enzymes have been identified in different bacteria. Each enzyme is named after the bacterium from which it was isolated using a naming system based on bacterial genus, species and strain.^[39]^[40] For example, the name of the EcoRI restriction enzyme was derived as shown in the box.

Applications

See the main article on restriction digests.

Isolated restriction enzymes are used to manipulate DNA for different scientific applications.

They are used to assist insertion of genes into plasmid vectors during gene cloning and protein expression experiments. For optimal use, plasmids that are commonly used for gene cloning are modified to include a short polylinker sequence (called the multiple cloning site, or MCS) rich in restriction enzyme recognition sequences. This allows flexibility when inserting gene fragments into the plasmid vector; restriction sites contained naturally within genes influence the choice of endonuclease for digesting the DNA since it is necessary to avoid restriction of wanted DNA while intentionally cutting the ends of the DNA. To clone a gene fragment into a vector, both plasmid DNA and gene insert are typically cut with the same restriction enzymes, and then glued together with the assistance of an enzyme known as a DNA ligase.^[41]^[42]

Restriction enzymes can also be used to distinguish gene alleles by specifically recognizing single base changes in DNA known as single nucleotide polymorphisms (SNPs).^[43]^[44] This is only possible if a SNP alters the restriction site present in the allele. In this method, the restriction enzyme can be used to genotype a DNA sample without the need for expensive gene sequencing. The sample is first digested with the restriction enzyme to generate DNA fragments, and then the different sized fragments separated by gel electrophoresis. In general, alleles with correct restriction sites will generate two visible bands of DNA on the gel, and those with altered restriction sites will not be cut and will generate only a single band. The number of bands reveals the sample subject's genotype, an example of restriction mapping.^{[citation needed]}

In a similar manner, restriction enzymes are used to digest genomic DNA for gene analysis by Southern blot. This technique allows researchers to identify how many copies (or paralogues) of a gene are present in the genome of one individual, or how many gene mutations (polymorphisms) have occurred within a population. The latter example is called restriction fragment length polymorphism (RFLP).^[45]

Examples

See the main article on list of restriction enzyme cutting sites.

Examples of restriction enzymes include:^[46]

Enzyme	Source	Recognition Sequence	Cut
EcoRI	Escherichia coli	5'GAATTC 3'CTTAAG	5'---G AATTC---3' 3'---CTTAA G---5'
EcoRII	Escherichia coli	5'CCWGG 3'GGWCC	5'--- CCWGG---3' 3'---GGWCC ---5'
BamHI	Bacillus amyloliquefaciens	5'GGATCC 3'CCTAGG	5'---G GATCC---3' 3'---CCTAG G---5'
HindIII	Haemophilus influenzae	5'AAGCTT 3'TTCGAA	5'---A AGCTT---3' 3'---TTCGA A---5'
TaqI	Thermus aquaticus	5'TCGA 3'AGCT	5'---T CGA---3' 3'---AGC T---5'
NotI	Nocardia otitidis	5'GCGGCCGC 3'CGCCGGCG	5'---GC GGCCGC---3' 3'---CGCCGG CG---5'
HinfI	Haemophilus influenzae	5'GANTCA 3'CTNAGT	5'---G ANTC---3' 3'---CTNA G---5'
Sau3A	Staphylococcus aureus	5'GATC 3'CTAG	5'--- GATC---3' 3'---CTAG ---5'
PovII*	Proteus vulgaris	5'CAGCTG 3'GTCGAC	5'---CAG CTG---3' 3'---GTC GAC---5'
SmaI*	Serratia marcescens	5'CCCGGG 3'GGGCCC	5'---CCC GGG---3' 3'---GGG CCC---5'
HaeIII*	Haemophilus aegyptius	5'GGCC 3'CCGG	5'---GG CC---3' 3'---CC GG---5'
HgaI^[47]	Haemophilus gallinarum	5'GACGC 3'CTGCG	5'---NN NN---3' 3'---NN NN---5'
AluI*	Arthrobacter luteus	5'AGCT 3'TCGA	5'---AG CT---3' 3'---TC GA---5'
EcoRV*	Escherichia coli	5'GATATC 3'CTATAG	5'---GAT ATC---3' 3'---CTA TAG---5'
EcoP15I	Escherichia coli	5'CAGCAGN₂₅NN 3'GTCGTCN₂₅NN	5'---CAGCAGN₂₅NN ---3' 3'---GTCGTCN₂₅ NN---5'
KpnI^[48]	Klebsiella pneumoniae	5'GGTACC 3'CCATGG	5'---GGTAC C---3' 3'---C CATGG---5'
PstI^[48]	Providencia stuartii	5'CTGCAG 3'GACGTC	5'---CTGCA G---3' 3'---G ACGTC---5'
SacI^[48]	Streptomyces achromogenes	5'GAGCTC 3'CTCGAG	5'---GAGCT C---3' 3'---C TCGAG---5'
SalI^[48]	Streptomyces albus	5'GTCGAC 3'CAGCTG	5'---G TCGAC---3' 3'---CAGCT G---5'
ScaI^[48]	Streptomyces caespitosus	5'AGTACT 3'TCATGA	5'---AGT ACT---3' 3'---TCA TGA---5'
SpeI	Sphaerotilus natans	5'ACTAGT 3'TGATCA	5'---A CTAGT---3' 3'---TGATC A---5'
SphI^[48]	Streptomyces phaeochromogenes	5'GCATGC 3'CGTACG	5'---GCATG C---3' 3'---C GTACG---5'
StuI^[49]^[50]	Streptomyces tubercidicus	5'AGGCCT 3'TCCGGA	5'---AGG CCT---3' 3'---TCC GGA---5'
XbaI^[48]	Xanthomonas badrii	5'TCTAGA 3'AGATCT	5'---T CTAGA---3' 3'---AGATC T---5'

Key:
* = blunt ends
N = C or G or T or A
W = A or T

References

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External links

General:

MeSH DNA Restriction Enzymes
Firman K (2007-11-24). "Type I Restriction-Modification". University of Portsmouth. http://www.typei-rm.info. Retrieved 2008-06-06.
Goodsell DS (2000-08-01). "Restriction Enzymes". Molecule of the Month. RCSB Protein Data Bank. http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb8_1.html. Retrieved 2008-06-06.
Simmer M, Secko D (2003-08-01). "Restriction Endonucleases: Molecular Scissors for Specifically Cutting DNA". The Science Creative Quarterly. http://www.scq.ubc.ca/?p=249. Retrieved 2008-06-06.

Databases:

Roberts RJ, Vincze T, Posfai, J, Macelis D. "REBASE". http://rebase.neb.com. Retrieved 2008-06-06. "Restriction Enzyme Database"

Software:

Bikandi J, San Millán R, Rementeria A, and Garaizar J. "Restriction enzyme digest of DNA". insilico.ehu.es. http://insilico.ehu.es/restriction. Retrieved 2008-06-06.
Palmer M. "WatCut". University of Waterloo, Ontario, Canada. http://watcut.uwaterloo.ca/watcut/watcut/template.php. Retrieved 2008-06-06. "An on-line tool for restriction analysis, silent mutation scanning, SNP-RFLP analysis"
Vincze,T, Posfai J, Roberts RJ. "NEBcutter V2.0". New England Biolabs Inc.. http://tools.neb.com/NEBcutter2/index.php. Retrieved 2008-06-06. "Restriction enzyme finder"
"Restriction enzyme digest of DNA software". BioPHP: PHP for Bioinformatics. http://www.biophp.org/minitools/restriction_digest/demo.php. Retrieved 2008-06-06. "Online tool, free source code"
"pDRAW32". AcaClone software. http://www.acaclone.com. Retrieved 2008-06-06. "Freeware DNA cloning, sequence analysis and plasmid/DNA plotting software"

Hydrolase: esterases (EC 3.1)

3.1.1: Carboxylic ester hydrolases

Cholinesterase (Acetylcholinesterase, Butyrylcholinesterase) · Pectinesterase · 6-phosphogluconolactonase · PAF acetylhydrolase

Lipase (Bile salt-dependent, Gastric/Lingual, Pancreatic, Lysosomal, Hormone-sensitive, Endothelial, Hepatic, Lipoprotein, Monoacylglycerol, Diacylglycerol)

Phospholipase (A1, A2, B)

3.1.2: Thioesterase

Palmitoyl protein thioesterase · Ubiquitin carboxy-terminal hydrolase L1

3.1.3: Phosphatase

Alkaline phosphatase (ALPI, ALPL, ALPP) · Acid phosphatase (Prostatic)/Tartrate-resistant acid phosphatase/Purple acid phosphatases · Nucleotidase · Glucose 6-phosphatase · Fructose 1,6-bisphosphatase · Calcineurin · Phosphoprotein phosphatase (PP2A) · OCRL · Pyruvate dehydrogenase phosphatase · Fructose 6-P,2-kinase:fructose 2,6-bisphosphatase · PTEN · Phytase · Inositol-phosphate phosphatase (IMPA1)

Phosphoprotein phosphatase: Protein tyrosine phosphatase · Protein serine/threonine phosphatase · Dual-specificity phosphatase

3.1.4: Phosphodiesterase

Autotaxin · Phospholipase (C, D) · Sphingomyelin phosphodiesterase (1) · PDE1 · PDE2 · PDE3 · PDE4A/PDE4B · PDE5 · Lecithinase (Clostridium perfringens alpha toxin) · Cyclic nucleotide phosphodiesterase

3.1.6: Sulfatase

arylsulfatase (Arylsulfatase A, Arylsulfatase B, Arylsulfatase E, Steroid sulfatase) · Galactosamine-6 sulfatase · Iduronate-2-sulfatase · N-acetylglucosamine-6-sulfatase

Nuclease (includes
deoxyribonuclease and
ribonuclease)

3.1.11-16: Exonuclease

Exodeoxyribonuclease	RecBCD

Exoribonuclease	Oligonucleotidase

3.1.21-31: Endonuclease

Endodeoxyribonuclease	Deoxyribonuclease I · Deoxyribonuclease II · Deoxyribonuclease IV · Restriction enzyme · UvrABC endonuclease

Endoribonuclease	RNase III · RNase H (1, 2A, 2B, 2C) · RNase P · RNase A (1, 2, 3, 4/5) · RNase T1 · RNA-induced silencing complex

either deoxy- or ribo-	Aspergillus nuclease S1 · Micrococcal nuclease

B enzm: 1.1/2/3/4/5/6/7/8/10/11/13/14/15-18, 2.1/2/3/4/5/6/7/8, 2.7.10, 2.7.11-12, 3.1/2/3/4/5/6/7, 3.1.3.48, 3.4.21/22/23/24, 4.1/2/3/4/5/6, 5.1/2/3/4/99, 6.1-3/4/5-6

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restriction enzyme