Micrococcal nuclease

Micrococcal nuclease
Ribbon schematic of micrococcal nuclease 3D structure, with Ca2+ and TdtP inhibitor
Identifiers
EC no.	3.1.31.1
CAS no.	9013-53-0
Databases
IntEnz	IntEnz view
BRENDA	BRENDA entry
ExPASy	NiceZyme view
KEGG	KEGG entry
MetaCyc	metabolic pathway
PRIAM	profile
PDB structures	RCSB PDB PDBe PDBsum
Search PMC articles PubMed articles NCBI proteins

Thermonuclease
Identifiers
Organism	Staphylococcus aureus
Symbol	nuc
UniProt	P00644
Search for Structures Swiss-model Domains InterPro

Staphylococcal nuclease
Identifiers
Symbol	?
Pfam	PF00565
InterPro	IPR016071
PROSITE	PDOC00865
CATH	1tt2
SCOP2	1tt2 / SCOPe / SUPFAM
Available protein structures: Pfam   structures / ECOD   PDB RCSB PDB; PDBe; PDBj PDBsum structure summary

Micrococcal nuclease (EC 3.1.31.1, S7 Nuclease , MNase, spleen endonuclease, thermonuclease, nuclease T, micrococcal endonuclease, nuclease T', staphylococcal nuclease, spleen phosphodiesterase, Staphylococcus aureus nuclease, Staphylococcus aureus nuclease B, ribonucleate (deoxynucleate) 3'-nucleotidohydrolase) is an endo-exonuclease that preferentially digests single-stranded nucleic acids. The rate of cleavage is 30 times greater at the 5' side of A or T than at G or C and results in the production of mononucleotides and oligonucleotides with terminal 3'-phosphates. ^[1] The enzyme is also active against double-stranded DNA and RNA and all sequences will be ultimately cleaved.

Characteristics

The enzyme has a molecular weight of 16.9kDa. The pH optimum is reported as 9.2. The enzyme activity is strictly dependent on Ca²⁺ and the pH optimum varies according to Ca²⁺ concentration. ^[2] The enzyme is therefore easily inactivated by EGTA.

Sources

This enzyme is the extracellular nuclease of Staphylococcus aureus . Two strains, V8 and Foggi, yield almost identical enzymes. ^[3] A common source is E.coli cells carrying a cloned nuc gene encoding Staphylococcus aureus extracellular nuclease (micrococcal nuclease).

Structure

The 3-dimensional structure of micrococcal nuclease (then called Staphyloccal nuclease) was solved very early in the history of protein crystallography, in 1969. ^[4] Higher-resolution, more recent crystal structures are available for the apo form ^[5] and for the thymidine-diphosphate-inhibited form. ^{[6] [7]} As seen in the ribbon diagram above, the nuclease molecule has 3 long alpha helices and a 5-stranded, barrel-shaped beta sheet, in an arrangement known as the OB-fold (for oligonucleotide-binding fold) as classified in the SCOP database.

Applications

• CUT&RUN sequencing, antibody-targeted controlled cleavage by micrococcal nuclease for transcriptomic profiling.
• Hydrolysis of nucleic acids in crude cell-free extracts.
• Sequencing of RNA.
• Preparation of rabbit reticulocyte lysates.
• Studies of chromatin structure.
• Removal of nucleic acids from laboratory protein preparations allowing for protein folding and structure-function studies.
• Research on the mechanisms of protein folding.

See also

• Serratia marcescens nuclease

References

1. Colin Dingwall, George P. Lomonossoff, Ronald A. Laskey, High sequence specificity of micrococcal nuclease, Nucleic Acids Research, Volume 9, Issue 12, 25 June 1981, Pages 2659–2674, https://doi.org/10.1093/nar/9.12.2659
2. Heins JN, Suriano JR, Taniuchi H, Anfinsen CB (1967). "Characterization of a nuclease produced by Staphylococcus aureus". J. Biol. Chem. 242 (5): 1016–20. doi: 10.1016/S0021-9258(18)96225-3 . PMID   6020427.
3. Cusumano CL, Taniuchi H, Anfinsen CB (1968). "Staphylococcal nuclease (Foggi strain). I. Order of cyanogen bromide fragments and a "fourth" histidine residue". J. Biol. Chem. 243 (18): 4769–77. doi: 10.1016/S0021-9258(18)93185-6 . PMID   5687719.
4. Arnone A, Bier J, et al. (1971). "A High Resolution Structure of an Inhibitor Complex of the Extracellular Nuclease of Staphylococcus aureus: I. Experimental Procedures and Chain Tracing". J. Biol. Chem. 246 (7): 2303–2316. doi: 10.1016/S0021-9258(19)77221-4 . PMID   5555571.
5. Truckses, D.M., Prehoda, K.E., Miller, S.C., Markley, J.L. and Somoza, J.R. (1996), Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease. Protein Science, 5: 1907-1916. https://doi.org/10.1002/pro.5560050917 PDB: https://www.rcsb.org/structure/1SNO
6. Khangulov, V.S., Schlessman, J.L., Heroux, A., Garcia-Moreno, E.B. Crystal structure of Staphylococcal nuclease variant Delta+PHS V104E at cryogenic temperature PDB: https://www.rcsb.org/structure/3H6M
7. Loll, P.J. and Lattman, E.E. (1989), The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+ and the inhibitor pdTp, refined at 1.65 Å. Proteins, 5: 183-201. https://doi.org/10.1002/prot.340050302 PDB: https://www.rcsb.org/structure/1SNC

• http://www.thermoscientificbio.com/dna-and-rna-modifying-enzymes/micrococcal-nuclease/
• http://www.worthington-biochem.com/NFCP/default.html
• http://www.thermoscientificbio.com/uploadedFiles/Resources/en0181-usa-msds.pdf - A material and safety data sheet for the product
• http://www.thermoscientificbio.com/uploadedFiles/Resources/en018-product-information.pdf - A Product Information sheet

External links

• Micrococcal+Nuclease at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
• EC 3.1.31.1