A restriction enzyme, restriction endonuclease, REase, ENase orrestrictase is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class of the broader endonuclease group of enzymes. Restriction enzymes are commonly classified into five types, which differ in their structure and whether they cut their DNA substrate at their recognition site, or if the recognition and cleavage sites are separate from one another. To cut DNA, all restriction enzymes make two incisions, once through each sugar-phosphate backbone of the DNA double helix.
In biochemistry, the DNA methyltransferase family of enzymes catalyze the transfer of a methyl group to DNA. DNA methylation serves a wide variety of biological functions. All the known DNA methyltransferases use S-adenosyl methionine (SAM) as the methyl donor.
Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Rossmann fold for binding S-Adenosyl methionine (SAM). Class II methyltransferases contain a SET domain, which are exemplified by SET domain histone methyltransferases, and class III methyltransferases, which are membrane associated. Methyltransferases can also be grouped as different types utilizing different substrates in methyl transfer reactions. These types include protein methyltransferases, DNA/RNA methyltransferases, natural product methyltransferases, and non-SAM dependent methyltransferases. SAM is the classical methyl donor for methyltransferases, however, examples of other methyl donors are seen in nature. The general mechanism for methyl transfer is a SN2-like nucleophilic attack where the methionine sulfur serves as the leaving group and the methyl group attached to it acts as the electrophile that transfers the methyl group to the enzyme substrate. SAM is converted to S-Adenosyl homocysteine (SAH) during this process. The breaking of the SAM-methyl bond and the formation of the substrate-methyl bond happen nearly simultaneously. These enzymatic reactions are found in many pathways and are implicated in genetic diseases, cancer, and metabolic diseases. Another type of methyl transfer is the radical S-Adenosyl methionine (SAM) which is the methylation of unactivated carbon atoms in primary metabolites, proteins, lipids, and RNA.
Type I site-specific deoxyribonuclease is an enzyme. This enzyme catalyses the following chemical reaction
DNA adenine methylase, (Dam methylase) (also site-specific DNA-methyltransferase (adenine-specific), EC 2.1.1.72, modification methylase, restriction-modification system) is an enzyme that adds a methyl group to the adenine of the sequence 5'-GATC-3' in newly synthesized DNA. Immediately after DNA synthesis, the daughter strand remains unmethylated for a short time. It is an orphan methyltransferase that is not part of a restriction-modification system and regulates gene expression. This enzyme catalyses the following chemical reaction
In enzymology, a tRNA (guanine-N1-)-methyltransferase (EC 2.1.1.31) is an enzyme that catalyzes the chemical reaction
In enzymology, a tRNA (guanine-N2-)-methyltransferase (EC 2.1.1.32) is an enzyme that catalyzes the chemical reaction
In enzymology, a tRNA (guanine-N7-)-methyltransferase (EC 2.1.1.33) is an enzyme that catalyzes the chemical reaction
PstI is a type II restriction endonuclease isolated from the Gram negative species, Providencia stuartii.
In molecular biology, REBASE is a database of information about restriction enzymes and DNA methyltransferases. REBASE contains an extensive set of references, sites of recognition and cleavage, sequences and structures. It also contains information on the commercial availability of each enzyme. REBASE is one of the longest running biological databases having its roots in a collection of restriction enzymes maintained by Richard J. Roberts since before 1980. Since that time there have been regular descriptions of the resource in the journal Nucleic Acids Research.
16S rRNA (cytosine1402-N4)-methyltransferase (EC 2.1.1.199, RsmH, MraW) is an enzyme with systematic name S-adenosyl-L-methionine:16S rRNA (cytosine1402-N4)-methyltransferase. This enzyme catalyses the following chemical reaction
Multisite-specific tRNA:(cytosine-C5)-methyltransferase is an enzyme with systematic name S-adenosyl-L-methionine:tRNA (cytosine-C5)-methyltransferase. This enzyme catalyses the following chemical reaction
TRNA (adenine57-N1/adenine58-N1)-methyltransferase (EC 2.1.1.219, TrmI, PabTrmI, AqTrmI, MtTrmI) is an enzyme with systematic name S-adenosyl-L-methionine:tRNA (adenine57/adenine58-N1)-methyltransferase. This enzyme catalyses the following chemical reaction:
DNA base flipping, or nucleotide flipping, is a mechanism in which a single nucleotide base, or nucleobase, is rotated outside the nucleic acid double helix. This occurs when a nucleic acid-processing enzyme needs access to the base to perform work on it, such as its excision for replacement with another base during DNA repair. It was first observed in 1994 using X-ray crystallography in a methyltransferase enzyme catalyzing methylation of a cytosine base in DNA. Since then, it has been shown to be used by different enzymes in many biological processes such as DNA methylation, various DNA repair mechanisms, and DNA replication. It can also occur in RNA double helices or in the DNA:RNA intermediates formed during RNA transcription.
