Endonuclease: Difference between revisions

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== Function ==
== Function ==


'''Endonuclease''' (ENN) cleaves phosphodiester bond within polynucleotide chain.  ENN cleaves DNA at a restriction site which is usually a 6-nucleotide palindrome.  ENN is restriction site–specific.  Various types of ENN differ by their mechanism of action.  ENN is used in genetic engineering to make recombinant DNA.  ENN requires a restriction site and a cleavage pattern.  '''ENN-I''' operates on DNA with separate restriction site and cleavage pattern, while '''ENN-II''' operates on overlapping restriction site and cleavage pattern.  Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN<ref>PMID:12483517</ref>.<br />
'''Endonuclease''' (ENN) cleaves phosphodiester bond within polynucleotide chain.  ENN cleaves DNA at a restriction site which is usually a 6-nucleotide palindrome.  ENN is restriction site–specific.  Various types of ENN differ by their mechanism of action.  ENN is used in genetic engineering to make recombinant DNA.  ENN requires a restriction site and a cleavage pattern.   
*'''ENN-I''' operates on DNA with separate restriction site and cleavage pattern.
*'''ENN-II''' operates on overlapping restriction site and cleavage pattern.   
*'''ENN-III''' is a bifunctional DNA glycosylase that removes oxidized pyrimidines from DNA<ref>PMID:30959406</ref>.
*'''ENN-IV''' cleaves the DNA backbone 5' of AP sites<ref>PMID:10458614</ref>.
*'''ENN-V''' removes deaminated bases from DNA<ref>PMID:23263163</ref>.
*'''ENN-VII''' recognizes mixmatches in DNA recombinational heteroduplexes and performs their incision<ref>PMID:21237725</ref>.
*'''ENN-VIII''' removes radiolysis thymine products from phage DNA and cleaves the DNA at AP sites<ref>PMID:9405426</ref>.
*'''Structure-specific ENN''' specific for DNA secondary structure rather than for its sequence<ref>PMID:28327556</ref>.
*'''Intron-encoded ENN''' or '''homing ENN''' are encoded by genes with mobile, self-splicing introns. They promote the movement of DNA sequences from one chromosome location to another<ref>PMID:9665136</ref>. <br />
The '''Cas ENN''' proteins are part of '''CRISPR/Cas''' prokaryotic immune system which confers protection from foreign genetic elements like viruses.  The '''CRISPR''' ('''C'''lustered '''R'''egularly '''I'''nterspersed '''S'''hort '''P'''alindromic '''R'''epeats) are DNA loci which are found in ca. 40% of the bacteria.  The CRISPR/Cas system is being used lately as gene editing tool<ref>PMID:20056882</ref>.  For more details see<br />
The '''Cas ENN''' proteins are part of '''CRISPR/Cas''' prokaryotic immune system which confers protection from foreign genetic elements like viruses.  The '''CRISPR''' ('''C'''lustered '''R'''egularly '''I'''nterspersed '''S'''hort '''P'''alindromic '''R'''epeats) are DNA loci which are found in ca. 40% of the bacteria.  The CRISPR/Cas system is being used lately as gene editing tool<ref>PMID:20056882</ref>.  For more details see<br />
*[[CRISPR-Cas]]
*[[CRISPR-Cas]]
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*CRISPR type V (Cpf1, C2c1, C2c3) - see [[CRISPR type V]]
*CRISPR type V (Cpf1, C2c1, C2c3) - see [[CRISPR type V]]
*CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see [[CRISPR type VI]]
*CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see [[CRISPR type VI]]
'''Intron-encoded ENN''' or '''homing ENN''' are encoded by genes with mobile, self-splicing introns. They promote the movement of DNA sequences from one chromosome location to another<ref>PMID:9665136</ref>. <br /> 
See also<br />
See also<br />
* [[Apurinic-Apyrimidinic Endonuclease-1]]<br />
* [[Apurinic-Apyrimidinic Endonuclease-1]]<br />

Latest revision as of 10:47, 18 June 2024


Function

Endonuclease (ENN) cleaves phosphodiester bond within polynucleotide chain. ENN cleaves DNA at a restriction site which is usually a 6-nucleotide palindrome. ENN is restriction site–specific. Various types of ENN differ by their mechanism of action. ENN is used in genetic engineering to make recombinant DNA. ENN requires a restriction site and a cleavage pattern.

  • ENN-I operates on DNA with separate restriction site and cleavage pattern.
  • ENN-II operates on overlapping restriction site and cleavage pattern.
  • ENN-III is a bifunctional DNA glycosylase that removes oxidized pyrimidines from DNA[1].
  • ENN-IV cleaves the DNA backbone 5' of AP sites[2].
  • ENN-V removes deaminated bases from DNA[3].
  • ENN-VII recognizes mixmatches in DNA recombinational heteroduplexes and performs their incision[4].
  • ENN-VIII removes radiolysis thymine products from phage DNA and cleaves the DNA at AP sites[5].
  • Structure-specific ENN specific for DNA secondary structure rather than for its sequence[6].
  • Intron-encoded ENN or homing ENN are encoded by genes with mobile, self-splicing introns. They promote the movement of DNA sequences from one chromosome location to another[7].

The Cas ENN proteins are part of CRISPR/Cas prokaryotic immune system which confers protection from foreign genetic elements like viruses. The CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) are DNA loci which are found in ca. 40% of the bacteria. The CRISPR/Cas system is being used lately as gene editing tool[8]. For more details see

See also

Relevance

Sickle cell anemia is caused by mutation in the recognition site of MstII ENN.

Disease

Mutation in UV-specific ENN causes Xeroderma pigmentosa. Mutations in tRNA-splicing ENN cause pontocerebellar hypoplasia.

Structural highlights

(PDB code 1rva).

3D structures of endonuclease

Endonuclease 3D structures


E. coli EcoRV endonuclease dimer (magenta, green) complex with DNA, (PDB code 1rva)

Drag the structure with the mouse to rotate

ReferencesReferences

  1. ↑ Sarre A, Stelter M, Rollo F, De Bonis S, Seck A, Hognon C, Ravanat JL, Monari A, Dehez F, Moe E, Timmins J. The three Endonuclease III variants of Deinococcus radiodurans possess distinct and complementary DNA repair activities. DNA Repair (Amst). 2019 Jun;78:45-59. PMID:30959406 doi:10.1016/j.dnarep.2019.03.014
  2. ↑ Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell. 1999 Aug 6;98(3):397-408. PMID:10458614
  3. ↑ Cao W. Endonuclease V: an unusual enzyme for repair of DNA deamination. Cell Mol Life Sci. 2013 Sep;70(17):3145-56. PMID:23263163 doi:10.1007/s00018-012-1222-z
  4. ↑ Shcherbakov VP, Plugina L, Shcherbakova T. Endonuclease VII is a key component of the mismatch repair mechanism in bacteriophage T4. DNA Repair (Amst). 2011 Apr 3;10(4):356-62. PMID:21237725 doi:10.1016/j.dnarep.2010.12.006
  5. ↑ Jiang D, Hatahet Z, Melamede RJ, Kow YW, Wallace SS. Characterization of Escherichia coli endonuclease VIII. J Biol Chem. 1997 Dec 19;272(51):32230-9. PMID:9405426
  6. ↑ Dehé PM, Gaillard PHL. Control of structure-specific endonucleases to maintain genome stability. Nat Rev Mol Cell Biol. 2017 May;18(5):315-330. PMID:28327556 doi:10.1038/nrm.2016.177
  7. ↑ Flick KE, Jurica MS, Monnat RJ Jr, Stoddard BL. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature. 1998 Jul 2;394(6688):96-101. PMID:9665136 doi:10.1038/27952
  8. ↑ Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010 Jan 8;327(5962):167-70. doi: 10.1126/science.1179555. PMID:20056882 doi:http://dx.doi.org/10.1126/science.1179555

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