6OZR

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 Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 76: 44

  • DOI: 10.1016/j.molcel.2019.06.046
  • Primary Citation of Related Structures:  
    6OZR, 6OZQ, 6OZS, 6OZJ, 6OZI, 6OZL, 6OZK, 6OZN, 6OZM, 6OZP

  • 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 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) ...

    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. Electronic address: wei.yang@nih.gov.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Endonuclease VA, B253Mus musculusMutation(s): 0 
Gene Names: Endov
EC: 3.1.26
UniProt
Find proteins for Q8C9A2 (Mus musculus)
Explore Q8C9A2 
Go to UniProtKB:  Q8C9A2
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by: Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA/RNA (23-MER)C, D23synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
K [auth A], Q [auth B]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
TLA
Query on TLA

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], P [auth B]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A], J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
L [auth A], M [auth A], R [auth B], S [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A], O [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], N [auth B], T [auth C], U [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.078α = 90
b = 72.663β = 90
c = 154.574γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-04
    Type: Initial release
  • Version 1.1: 2019-10-16
    Changes: Data collection, Database references