Endonuclease

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].

Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN^[4].
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^[5]. For more details see

• CRISPR-Cas
• CRISPR type I-A (Cascade) - see CRISPR subtype I-A
• CRISPR type I-B (Cascade) - see CRISPR subtype I-B
• CRISPR type I-C (Cascade) - see CRISPR subtype I-C
• CRISPR type I-E (Cascade) - see CRISPR subtype I-E
• (CRISPR type I-F (Csy1, Csy2, Csy3) - see CRISPR subtype I-F
• CRISPR type III-A (Csm complex) - see CRISPR subtype III-A (Csm complex)
• CRISPR type II-A - see CRISPR-Cas9
• 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

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^[6].
See also

• Apurinic-Apyrimidinic Endonuclease-1
  
• For EcoRV ENN see Student Projects for UMass Chemistry 423 Spring 2012-3
  
• For NEI ENN see DNA repair protein human endonuclease VIII-like 1 (NEIL1).

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