Nuclease S1 () is an

endonuclease Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain. Some, such as deoxyribonuclease I, cut DNA relatively nonspecifically (without regard to sequence), while many, typically called restriction endonuclease ...

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecule ...

that splits single-stranded DNA (ssDNA) and RNA into oligo- or mononucleotides. This enzyme catalyses the following

chemical reaction A chemical reaction is a process that leads to the chemical transformation of one set of chemical substances to another. Classically, chemical reactions encompass changes that only involve the positions of electrons in the forming and break ...

: Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products Although its primary substrate is single-stranded, it can also occasionally introduce single-stranded breaks in double-stranded DNA or RNA, or DNA-RNA hybrids. The enzyme hydrolyses single stranded region in duplex DNA such as loops or gaps. It also cleaves a strand opposite a nick on the complementary strand. It has no sequence specificity. Well-known versions include S1 found in ''

Aspergillus oryzae ''Aspergillus oryzae'', also known as , is a filamentous fungus (a mold) used in East Asia to saccharify rice, sweet potato, and barley in the making of alcoholic beverages such as '' sake'' and ''shōchū'', and also to ferment soybeans f ...

'' (yellow koji mold) and Nuclease P1 found in ''

Penicillium citrinum ''Penicillium citrinum'' is an anamorph, mesophilic fungus species of the genus of '' Penicillium'' which produces tanzawaic acid A-D, ACC, Mevastatin, Quinocitrinine A, Quinocitrinine B, and nephrotoxic citrinin Citrinin is a mycotoxin ...

''. Members of the S1/P1 family are found in both

prokaryotes A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Conn ...

and

eukaryotes Eukaryotes () are organisms whose cells have a nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the three domains of life. Bact ...

and are thought to be associated in programmed cell death and also in tissue differentiation. Furthermore, they are secreted extracellular, that is, outside of the cell. Their function and distinguishing features mean they have potential in being exploited in the field of

biotechnology Biotechnology is the integration of natural sciences and engineering sciences in order to achieve the application of organisms, cells, parts thereof and molecular analogues for products and services. The term ''biotechnology'' was first used b ...

Nomenclature

Alternative names include endonuclease S1 (Aspergillus), single-stranded-nucleate endonuclease, deoxyribonuclease S1, deoxyribonuclease S1, Aspergillus nuclease S1, Neurospora crassa single-strand specific endonuclease, S1 nuclease, single-strand endodeoxyribonuclease, single-stranded DNA specific endonuclease, single-strand-specific endodeoxyribonuclease, single strand-specific DNase and Aspergillus oryzae S1 nuclease.

Structure

Most nucleases with EC 3.1.30.1 activity are homologous to each other in a

protein domain In molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist o ...

family called Nuclease S1/P1. Members of this family, including P1 and S1, are

glycoprotein Glycoproteins are proteins which contain oligosaccharide chains covalently attached to amino acid side-chains. The carbohydrate is attached to the protein in a cotranslational or posttranslational modification. This process is known as g ...

s with very distinguishing features, they are: * a requirement for three zinc ions cofactors, * containing common active site motifs and * requires an acidic pH for catalysis. * contains three

glycans The terms glycans and polysaccharides are defined by IUPAC as synonyms meaning "compounds consisting of a large number of monosaccharides linked glycosidically". However, in practice the term glycan may also be used to refer to the carbohydrat ...

bound to the

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha ...

asparagine via

N-glycosylation ''N''-linked glycosylation, is the attachment of an oligosaccharide, a carbohydrate consisting of several sugar molecules, sometimes also referred to as glycan, to a nitrogen atom (the amide nitrogen of an asparagine (Asn) residue of a protein) ...

* two Disulphide bridges between

cysteine Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. When present as a deprotonated catalytic residue, s ...

residues. These requirements and distinguishing features are responsible for function efficacy. It is an enzyme and these four features are needed for enzyme functionality. The three zinc ions are vital for catalysis. The first two zincs activate the attacking water in hydrolysis whilst the third zinc ion stabilizes the leaving oxyanion.

Properties

Aspergillus nuclease S1 is a monomeric protein of a molecular weight of 38 kilodalton. It requires Zn²⁺ as a cofactor and is relatively stable against denaturing agents like urea, SDS, or formaldehyde. The optimum pH for its activity lies between 4-4.5. Aspergillus nuclease S1 is known to be inhibited somewhat by 50 μM ATP and nearly completely by 1 mM ATP. 50% inhibition has been shown at 85 μM dAMP and 1 μM dATP but uninhibited by cAMP.

Mechanism

This zinc-dependent nuclease protein domain produces 5'

nucleotides Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules wi ...

and cleaves

phosphate In chemistry, a phosphate is an anion, salt, functional group or ester derived from a phosphoric acid. It most commonly means orthophosphate, a derivative of orthophosphoric acid . The phosphate or orthophosphate ion is derived from phosph ...

groups from 3' nucleotides. Additionally, the side chain of

tryptophan Tryptophan (symbol Trp or W) is an α-amino acid that is used in the biosynthesis of proteins. Tryptophan contains an α-amino group, an α-carboxylic acid group, and a side chain indole, making it a polar molecule with a non-polar aromati ...

located in the cavity in the active site and its backbone supports the action one of the zinc ions. Such mechanisms are essential to the catalytic function of the enzyme.

Uses

Aspergillus nuclease S1 is used in the laboratory as a reagent in nuclease protection assays. In molecular biology, it is used in removing single stranded tails from DNA molecules to create blunt ended molecules and opening hairpin loops generated during synthesis of double stranded cDNA.

Nomenclature

Structure

Properties

Mechanism

Uses

See also

References

Further reading