6OZG image
Deposition Date 2019-05-15
Release Date 2019-09-04
Last Version Date 2023-10-11
Entry Detail
PDB ID:
6OZG
Keywords:
HYDROLASE
Title:
Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89Q) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine
Biological Source:
Source Organism:
Thermotoga maritima (Taxon ID: 2336)
synthetic construct (Taxon ID: 32630)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.93 Å
R-Value Free:
0.20
R-Value Work:
0.17
R-Value Observed:
0.17
Space Group:
P 2 21 21
6OZG validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Endonuclease V
Gene (Uniprot):nfi
Mutagens:E89Q
Chain IDs:A, B
Chain Length:224
Number of Molecules:2
Biological Source:Thermotoga maritima
UniProt ID:Q9X2H9 Pfam ID:PF04493 EC:3.1.21.7
Polymer Type:polydeoxyribonucleotide/polyribonucleotide hybrid
Molecule:DNA/RNA (5'-D(*AP*AP*TP*GP*A)-R(P*A)-D(P*GP*AP*T)-R(P*NP*N)-D(P*T)-3')
Chain IDs:C, D
Chain Length:12
Number of Molecules:2
Biological Source:synthetic construct
Ligand Molecules
EDO
GOL
MG
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
6OZG