6OZF | pdb_00006ozf

Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine

• PDB DOI: https://doi.org/10.2210/pdb6OZF/pdb
• NAKB: 6OZF

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 1.80 Å
• R-Value Free: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.43 kDa 
• Atom Count: 4,478 
• Modeled Residue Count: 469 
• Deposited Residue Count: 474 
• Unique protein chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease V	A, B	225	Thermotoga maritima	Mutation(s): 1  Gene Names: nfi, TM_1865 EC: 3.1.21.7
UniProt
Find proteins for Q9X2H9 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9X2H9  Go to UniProtKB:  Q9X2H9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-D(P*AP*AP*TP*GP*I)-R(P*A)-D(P*GP*AP*TP*GP*CP*T)-3')	C, D	12	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	K [auth B]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
GOL	H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	J [auth B], N [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	E [auth A], G [auth B], M [auth C], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	F [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.129	α = 90
b = 75.578	β = 90
c = 106.397	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	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: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description