6OZI

Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 

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
244Ciona intestinalisMutation(s): 1 
Gene Names: LOC100181026
Find proteins for A0A3Q0JV13 (Ciona intestinalis)
Go to UniProtKB:  A0A3Q0JV13
Entity ID: 2
MoleculeChainsLengthOrganism
DNA/RNA (23-MER)C,D23synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
A, B
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.174 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 51.079α = 90.00
b = 81.428β = 90.00
c = 166.034γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
MOLREPphasing
HKL-2000data reduction
PDB_EXTRACTdata extraction

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