Micrococcal nuclease

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Micrococcal nuclease - Wikipedia

From Wikipedia, the free encyclopedia

Micrococcal nuclease

Ribbon schematic of micrococcal nuclease 3D structure, with Ca²⁺ and TdtP inhibitor

Identifiers

Databases

PDB structures

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

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. 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.^[1] 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.^[2] 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,^[3] deposited as now-obsolete Protein Data Bank file 1SNS. Higher-resolution, more recent crystal structures are available for the apo form as Protein Data Bank file 1SNO: [1] and for the thymidine-diphosphate-inhibited form as Protein Data Bank file 3H6M: [2] or 1SNC: [3]. 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.

References

^ 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.
^ 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.
^ 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.

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

Hydrolase: esterases (EC 3.1)

3.1.1: Carboxylic
ester hydrolases

Lipase

Phospholipase
- A1
- A2
- B

3.1.2: Thioesterase

3.1.3: Phosphatase

3.1.4:
Phosphodiesterase

3.1.6: 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;see {{Restriction enzyme}} UvrABC endonuclease
Endoribonuclease	RNase III Drosha: Microprocessor complex Dicer: RNA-induced silencing complex RNase H 1 2A 2B 2C RNase P RNase A RNase Z RNase E 1 2 3 4/5 RNase T1
either deoxy- or ribo-	Nuclease S1 Mung bean nuclease Serratia marcescens nuclease Micrococcal nuclease

v t e Enzymes
Activity	Active site Binding site Catalytic triad Oxyanion hole Enzyme promiscuity Diffusion-limited enzyme Cofactor Enzyme catalysis
Regulation	Allosteric regulation Cooperativity Enzyme inhibitor Enzyme activator
Classification	EC number Enzyme superfamily Enzyme family List of enzymes
Kinetics	Enzyme kinetics Eadie–Hofstee diagram Hanes–Woolf plot Lineweaver–Burk plot Michaelis–Menten kinetics
Types	EC1 Oxidoreductases (list) EC2 Transferases (list) EC3 Hydrolases (list) EC4 Lyases (list) EC5 Isomerases (list) EC6 Ligases (list) EC7 Translocases (list)

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Characteristics

Sources

Structure

Applications

See also

References

External links