6OZN image
Deposition Date 2019-05-15
Release Date 2019-09-04
Last Version Date 2024-03-13
Entry Detail
PDB ID:
6OZN
Keywords:
HYDROLASE/RNA
Title:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 15 min soak in 10 mM Mn2+
Biological Source:
Source Organism:
Mus musculus (Taxon ID: 10090)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.90 Å
R-Value Free:
0.22
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
6OZN validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Endonuclease V
Gene (Uniprot):Endov
Chain IDs:A, B
Chain Length:253
Number of Molecules:2
Biological Source:Mus musculus
UniProt ID:Q8C9A2 Pfam ID:PF04493 EC:3.1.21.7
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Molecule:DNA/RNA (5'-R(P*CP*GP*GP*UP*AP*AP*CP*CP*C)-D(P*I)-R(P*AP*UP*AP*UP*GP*CP*AP*UP*GP*CP*AP*UP*U)-3')
Chain IDs:C, D
Chain Length:23
Number of Molecules:2
Biological Source:synthetic construct
Ligand Molecules
EDO
GOL
MN
P6G
PG4
PGE
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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Disease

Primary Citation of related structures
6OZN