6OZK | pdb_00006ozk

Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after 68h soak in Ca2+

• PDB DOI: https://doi.org/10.2210/pdb6OZK/pdb
• NAKB: 6OZK

• Classification: HYDROLASE
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

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

• PubMed: 31444105 
• DOI: https://doi.org/10.1016/j.molcel.2019.06.046
• Primary Citation Related Structures: 
  6OZE, 6OZF, 6OZG, 6OZH, 6OZI, 6OZJ, 6OZK, 6OZL, 6OZM, 6OZN, 6OZO, 6OZP, 6OZQ, 6OZR, 6OZS


• 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). 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.

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Organizational Affiliation: 
• Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA.
Section on Biological Chemistry, NIDCR, NIH, Bethesda, MD 20892, USA.
Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan.
Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 70.64 kDa 
• Atom Count: 4,735 
• Modeled Residue Count: 520 
• Deposited Residue Count: 538 
• Unique protein chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease V	A, B	246	Mus musculus	Mutation(s): 0  Gene Names: Endov EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C9A2 (Mus musculus) Explore Q8C9A2  Go to UniProtKB:  Q8C9A2
IMPC:  MGI:2444688

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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')	C, D	23	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	Q [auth B], R [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
TLA	M [auth A], N [auth A], S [auth D]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
GOL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth A], F [auth A], O [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.214 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.823	α = 90
b = 73.012	β = 90
c = 155.229	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2019-09-04
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2024-03-13
  Changes: Data collection, Database references, Derived calculations, Refinement description