6OZH

Crystal structure of Ciona intestinalis (Ci) Endonuclease V in complex with a 24mer DNA containing an inosine followed by a ribo-adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.026 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.

Wu, J.Samara, N.L.Kuraoka, I.Yang, W.

(2019) Mol.Cell --: --

  • DOI: 10.1016/j.molcel.2019.06.046
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 si ...

    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 Mn 2+ 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.


    Organizational Affiliation

    Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA.,Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA. Electronic address: wei.yang@nih.gov.,Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan.,Section on Biological Chemistry, NIDCR, NIH, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
endonuclease V isoform X2
A, B, C, D
245Ciona intestinalisMutation(s): 0 
Gene Names: LOC100181026
Find proteins for A0A3Q0JV13 (Ciona intestinalis)
Go to UniProtKB:  A0A3Q0JV13
Entity ID: 2
MoleculeChainsLengthOrganism
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')E,F,G,H24synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.026 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.245α = 90.00
b = 121.975β = 98.75
c = 79.921γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-05-15 
  • Released Date: 2019-09-04 
  • Deposition Author(s): Samara, N.L., Yang, W.

Revision History 

  • Version 1.0: 2019-09-04
    Type: Initial release