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Structure paper

TitleEvolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.
Journal, issue, pagesMol. Cell, Vol. 76, Page 44-, Year 2019
Publish dateMay 15, 2019 (structure data deposition date)
AuthorsWu, J. / Samara, N.L. / Kuraoka, I. / Yang, W.
External linksMol. Cell / PubMed:31444105
MethodsX-ray diffraction
Resolution1.5 - 3.026 Å
Structure data

PDB-6oze:
Crystal structure of the catalytic domain of human Endonuclease V (C140S/C225S/C226A/C228S)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6ozf:
Crystal structure of Thermotoga maritima (Tm) Endonuclease V (D110N) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-6ozg:
Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89Q) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine
Method: X-RAY DIFFRACTION / Resolution: 1.93 Å

PDB-6ozh:
Crystal structure of Ciona intestinalis (Ci) Endonuclease V in complex with a 24mer DNA containing an inosine followed by a ribo-adenosine
Method: X-RAY DIFFRACTION / Resolution: 3.026 Å

PDB-6ozi:
Crystal structure of Ciona intestinalis (Ci) Endonuclease V (D234N) in complex with a 23mer DNA containing an inosine followed by a ribo-adenosine
Method: X-RAY DIFFRACTION / Resolution: 2.302 Å

PDB-6ozj:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine in the absence of divalent cation
Method: X-RAY DIFFRACTION / Resolution: 2.247 Å

PDB-6ozk:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after 68h soak in Ca2+
Method: X-RAY DIFFRACTION / Resolution: 2.104 Å

PDB-6ozl:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 2 min soak in Mn2+
Method: X-RAY DIFFRACTION / Resolution: 2.1 Å

PDB-6ozm:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 10 min soak in 10 mM Mn2+
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-6ozn:
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 Mn2+
Method: X-RAY DIFFRACTION / Resolution: 1.9 Å

PDB-6ozo:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 30 min soak in 10 mM Mn2+
Method: X-RAY DIFFRACTION / Resolution: 2.235 Å

PDB-6ozp:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 180 min soak in 10 mM Mn2+
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-6ozq:
Crystal structure of Mus musculus (Mm) Endonuclease V (K155M) in complex with a 23mer RNA oligo containing an inosine after a 100 min soak in 10 mM Mn2+ and K+
Method: X-RAY DIFFRACTION / Resolution: 2.153 Å

PDB-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+
Method: X-RAY DIFFRACTION / Resolution: 2.15 Å

PDB-6ozs:
Crystal structure of Mus musculus (Mm) Endonuclease V in complex with a 23mer RNA oligo containing an inosine after a 90 min soak in 10 mM Mg2+
Method: X-RAY DIFFRACTION / Resolution: 2.41 Å

Chemicals

ChemComp-ACT:
ACETATE ION / Acetate

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-NA:
Unknown entry

ChemComp-HOH:
WATER / Water

ChemComp-CA:
Unknown entry

ChemComp-EDO:
1,2-ETHANEDIOL / Ethylene glycol

ChemComp-PG4:
TETRAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

ChemComp-MG:
Unknown entry

ChemComp-K:
Unknown entry

ChemComp-PGE:
TRIETHYLENE GLYCOL / Polyethylene glycol

ChemComp-TLA:
L(+)-TARTARIC ACID / Tartaric acid

ChemComp-MN:
Unknown entry

ChemComp-P6G:
HEXAETHYLENE GLYCOL / precipitant*YM / Polyethylene glycol

Source
  • homo sapiens (human)
  • thermotoga maritima (bacteria)
  • synthetic construct (others)
  • ciona intestinalis (vase tunicate)
  • mus musculus (house mouse)
KeywordsHYDROLASE / Nucleic acid hydrolysis / RNA recognition / metal ion dependent catalysis / DNA damage / adenosine deamination / HYDROLASE/RNA / HYDROLASE-RNA complex

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