Deoxyribonuclease IV (phage-T4-induced) (EC 3.1.21.2, endodeoxyribonuclease IV (phage T4-induced), E. coli endonuclease IV, endodeoxyribonuclease, redoxyendonuclease, deoxriboendonuclease, Escherichia coli endonuclease II, endonuclease II, DNA-adenine-transferase) is catalyzes the degradation nucleotides[1] in DsDNA by attacking the 5'-terminal end.[2][3][4]
| Deoxyribonuclease IV (phage-T4-induced) | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| EC no. | 3.1.21.2 | ||||||||
| CAS no. | 63363-78-0 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| |||||||||
Deoxyribonuclease IV is a type of deoxyribonuclease that has both an exonucleolytic and an endonucleolytic activity.[1] It functions at abasic or apurinic-apyrimidinic sites when the cell is undergoing nucleotide excision repair pathway.[5] In addition, the endonuclease IV consists of several activities such as AP endonuclease, 3'-diesterase, 3'->5' exonuclease, and 3'phosphatase.[6]
The endonuclease IV is encoded by denB of bacteriophage T4 and its binding sequence is 5′-dT||dCdAdCdTdTdC-3′. It has been discovered that serine 176 residue plays a crucial role in increasing the hydrolysis rate of the endonuclease of a consensus sequence containing cytidine. The endonuclease IV falls under a structurally resembling members with apyrimidininc endonuclease I (APE1).[7]
Discovery
Deoxyribonuclease IV was first isolated from rabbit tissues in 1968. Specifically, it was found in rabbit bone marrow by Lindahl.[8] And its molecular weight was determined to be 42,000 dalton. It was discovered that this enzyme resembles several microbial endonuclease activities of DNA polymerase I found in Escherichia coli, which appear to be necessary for DNA repair and recombination.[9] It also resembles gamma exonuclease, which performs an important function in recombination of bacteriophage.[10]
Structure
DNase IV is composed of 185 amino acid residues with magnesium ions acting as a cofactor. Divalent metal ions such as Mg²⁺ act as cofactor during the cleavage of 5'-mononucleotides.[11] DNase IV prefers to attack native DNA acting as an endonuclease with metal ions either Mg++ or Mn++.[12] Its TIM beta barrel core surrounded by helices with three metal ions —either three Zn2+ or two Zn2+ and one Mn2+ which plays crucial role in AP excision repair.[13]
Function
DNase IV attacks dsDNA at 5' ends by liberating 5' mononucleotides but it does not attack any monomers in polydeoxyribonucleotides in a random fashion. It cleaves polydeoxyribonucleotides in an exonucleolytic fashion from 5' end, meaning it removes a nucleotide chain that is adjacent to the 5' terminal end rather than cleaving a nucleotide located in the middle of the chain. DNase IV works by attacking multiple polynucleotide chains at the same time.[10] Since it does not cleave dsDNA in a processive way, the rate of hydrolysis of this enzyme is faster than native DNA in terms of kinetics.[14] DNase IV does not recognize specific sequences on DNA for non-staggered cleavage. However, it requires two base pairs at one cleavage site, and the other cleavage site of double-stranded DNA should have more than 10 base pairs.[12]
Enzyme Activities in cell environment and DNA
70% of the total DNase IV activity was found in the cytoplasm while 30% was found in cell nuclei.[1] In human body, DNase IV was required for cleavage of a reaction intermediate generated by template strand displacement during gap-filling.[15]
During the endonuclease activity, conformational change in DNA occurs in a way that exposes the abasic site by bending the DNA by 90 degrees, which involves flipping out the sugar moiety into a small pocket that would not form watson-crick base pair.[13]
DNase IV acts on double stranded DNA in repair by breaking phosphodiester bonds, but the number of cleavages by this enzyme is smaller than the extent of polymerization of DNA.[14]
Difference between DNase III vs. DNase IV
In crude cell extracts from lymphoid organs, DNase III and DNase IV show major activities because DNase I activity is inhibited. The activities of DNase III and DNase IV depend on two Mg++ as cofactors and these enzymes are localized in cell nuclei. Even though they require same divalent metal to function, there are major difference in liberating polynucleotides. DNase III cleaves a single strand of DNA from 3' terminal end but DNase IV cleaves a double strand of DNA from 5' terminal end.[10] Because DNase III degrades single stranded DNA, the rate of hydrolysis of DNase III is more rapid than that of DNase IV.[1]
See also
References
External links
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