Deoxyribonuclease IV

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Deoxyribonuclease IV (phage-T4-induced)
Identifiers
EC no.3.1.21.2
CAS no.63363-78-0
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum

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 a kind of Endonuclease that catalyzes the degradation nucleotides[1] in DsDNA by attacking the 5'-terminal end.[2][3][4]

Deoxyribonuclease IV is a type of deoxyribonuclease that functions at abasic or apurinic-apyrimidininc 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, 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.[8]

Structure[]

DNase IV is composed of 185 amino acid residues with magnesium ions acting as a cofactor. Diavalent metal ion such as Mg²⁺ which acting as cofactor during the cleavage of 5'-mononucleotides.[9] 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.[10]

Enzyme Activities in cell environment and DNA[]

70% of the total DNase IV activitiy 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.[11]

During the endonuclease activity, conformational change in DNA occurs in a way that exposes the abasic site by benting the DNA by 90 degrees, which inovles flipping out the sugar moiety into a small pocket that would not form watson-crick base pair.[10]

See also[]

  • Phage T4

References[]

  1. ^ a b Robins P, Pappin DJ, Wood RD, Lindahl T (November 1994). "Structural and functional homology between mammalian DNase IV and the 5'-nuclease domain of Escherichia coli DNA polymerase I". The Journal of Biological Chemistry. 269 (46): 28535–8. doi:10.1016/s0021-9258(19)61935-6. PMID 7961795.
  2. ^ Friedberg EC, Goldthwait DA (March 1969). "Endonuclease II of E. coli. I. Isolation and purification". Proceedings of the National Academy of Sciences of the United States of America. 62 (3): 934–40. Bibcode:1969PNAS...62..934F. doi:10.1073/pnas.62.3.934. PMC 223688. PMID 4895219.
  3. ^ Hadi SM, Goldthwait DA (December 1971). "Endonuclease II of Escherichia coli. Degradation of partially depurinated deoxyribonucleic acid". Biochemistry. 10 (26): 4986–93. doi:10.1021/bi00802a024. PMID 4944066.
  4. ^ Sadowski PD, Hurwitz J (November 1969). "Enzymatic breakage of deoxyribonucleic acid. I. Purification and properties of endonuclease II from T4 phage-infected Escherichia coli". The Journal of Biological Chemistry. 244 (22): 6182–91. doi:10.1016/S0021-9258(18)63523-9. PMID 4310836.
  5. ^ Friedberg EC, Hadi SM, Goldthwait DA (November 1969). "Endonuclease II of Escherichia coli. II. Enzyme properties and studies on the degradation of alkylated and native deoxyribonucleic acid". The Journal of Biological Chemistry. 244 (21): 5879–89. doi:10.1016/S0021-9258(18)63556-2. PMID 4981786.
  6. ^ Kerins, Sinéad M.; Collins, Ruairi; McCarthy, Tommie V. (January 2003). "Characterization of an Endonuclease IV 3′-5′ Exonuclease Activity". Journal of Biological Chemistry. 278 (5): 3048–3054. doi:10.1074/jbc.m210750200. ISSN 0021-9258. PMID 12444080.
  7. ^ Hirano, N.; Ohshima, H.; Sakashita, H.; Takahashi, H. (2007-11-29). "The Ser176 of T4 endonuclease IV is crucial for the restricted and polarized dC-specific cleavage of single-stranded DNA implicated in restriction of dC-containing DNA in host Escherichia coli". Nucleic Acids Research. 35 (20): 6692–6700. doi:10.1093/nar/gkm722. ISSN 0305-1048. PMC 2175332. PMID 17913749.
  8. ^ Lindahl T, Gally JA, Edelman GM (February 1969). "Deoxyribonuclease IV: a new exonuclease from mammalian tissues". Proceedings of the National Academy of Sciences of the United States of America. 62 (2): 597–603. Bibcode:1969PNAS...62..597L. doi:10.1073/pnas.62.2.597. PMC 277851. PMID 5256235.
  9. ^ Mishra NC (1995). Molecular biology of nucleases. Boca Raton: CRC Press. ISBN 978-0-8493-7658-0. OCLC 31436640.
  10. ^ a b Tsutakawa, Susan E.; Lafrance-Vanasse, Julien; Tainer, John A. (2014-07-01). "The cutting edges in DNA repair, licensing, and fidelity: DNA and RNA repair nucleases sculpt DNA to measure twice, cut once". DNA Repair. 19: 95–107. doi:10.1016/j.dnarep.2014.03.022. ISSN 1568-7864. PMC 4051888. PMID 24754999.
  11. ^ Klungland A, Lindahl T (June 1997). "Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1)". The EMBO Journal. 16 (11): 3341–8. doi:10.1093/emboj/16.11.3341. PMC 1169950. PMID 9214649.

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