6OZH image
Deposition Date 2019-05-15
Release Date 2019-09-04
Last Version Date 2024-03-13
Entry Detail
PDB ID:
6OZH
Keywords:
HYDROLASE
Title:
Crystal structure of Ciona intestinalis (Ci) Endonuclease V in complex with a 24mer DNA containing an inosine followed by a ribo-adenosine
Biological Source:
Source Organism(s):
Ciona intestinalis (Taxon ID: 7719)
synthetic construct (Taxon ID: 32630)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.03 Å
R-Value Free:
0.26
R-Value Work:
0.23
R-Value Observed:
0.23
Space Group:
P 1 21 1
6OZH validation report
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:endonuclease V isoform X2
Chain IDs:A, B, C, D
Chain Length:245
Number of Molecules:4
Biological Source:Ciona intestinalis
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Molecule:DNA/RNA (5'-D(P*CP*GP*GP*TP*AP*AP*CP*CP*GP*I)-R(P*A)-D(P*TP*AP*TP*GP*CP*AP*GP*CP*AP*TP*TP*TP*C)-3')
Chain IDs:E, F, G, H
Chain Length:24
Number of Molecules:4
Biological Source:synthetic construct
Ligand Molecules
CA
Primary Citation
Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Mol.Cell 76 44 ? (2019)
PMID: 31444105 DOI: 10.1016/j.molcel.2019.06.046

Abstact

Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn2+ that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.

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Primary Citation of related structures
6OZH
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