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Structure paper

TitleNew structural insights reveal an expanded reaction cycle for inositol pyrophosphate hydrolysis by human DIPP1.
Journal, issue, pagesFaseb J., Vol. 35, Page e21275-e21275, Year 2021
Publish dateApr 24, 2020 (structure data deposition date)
AuthorsZong, G. / Jork, N. / Hostachy, S. / Fiedler, D. / Jessen, H.J. / Shears, S.B. / Wang, H.
External linksFaseb J. / PubMed:33475202
MethodsX-ray diffraction
Resolution1.35 - 2 Å
Structure data

PDB-6wo7:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-Diphosphoinositol pentakisphosphate (5-IP7), Mg, and Fluoride ion
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-6wo8:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-diphosphoinositol 1,3,4,6-tetrakisphosphate (5-PP-IP4), Mg, and Fluoride ion
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6wo9:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1-diphosphoinositol pentakisphosphate (1-IP7) and Mg
Method: X-RAY DIFFRACTION / Resolution: 2.0 Å

PDB-6woa:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 2-Diphosphoinositol pentakisphosphate (2-IP7), Mg, and Fluoride ion
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6wob:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 4-diphosphoinositol pentakisphosphate (4-IP7), Mg, and Fluoride ion
Method: X-RAY DIFFRACTION / Resolution: 1.45 Å

PDB-6woc:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-diphosphoinositol pentakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 1min in the absence of Fluoride.
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-6wod:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 2min in the absence of Fluoride.
Method: X-RAY DIFFRACTION / Resolution: 1.35 Å

PDB-6woe:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 10min in the absence of Fluoride.
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

PDB-6wof:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 20min in the absence of Fluoride.
Method: X-RAY DIFFRACTION / Resolution: 1.6 Å

PDB-6wog:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 5-methylenebisphosphonate inositol pentakisphosphate (5-PCP-IP5)
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-6woh:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1,5-di-methylenebisphosphonate inositol tetrakisphosphate (1,5-PCP-IP4)
Method: X-RAY DIFFRACTION / Resolution: 1.7 Å

PDB-6woi:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with 1-Diphosphoinositol pentakisphosphate, Mg, and Fluoride ion, presoaked with 1,5-IP8, Mg and Fluoride for 30 seconds
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

Chemicals

ChemComp-I7P:
(1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate

ChemComp-MG:
Unknown entry

ChemComp-CL:
Unknown entry / Chloride

ChemComp-F:
FLUORIDE ION / Fluoride

ChemComp-HOH:
WATER / Water

ChemComp-U6J:
(1r,2R,3S,4r,5R,6S)-4-hydroxy-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl trihydrogen diphosphate

ChemComp-SO4:
SULFATE ION / Sulfate

ChemComp-O81:
(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate

ChemComp-UEV:
(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate

ChemComp-U71:
(1S,2R,3S,4S,5S,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

ChemComp-5A3:
Methylenebisphosphonate inositol pentakisphosphate

ChemComp-4WZ:
{[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy)cyclohexane-1,3-diyl]bis[oxy(hydroxyphosphoryl)methanediyl]}bis(phosphonic acid)

Source
  • homo sapiens (human)
KeywordsHYDROLASE / phosphatase / nudix / catalysis mechanism / Substrate Specificity / inositol / inositol pyrophosphate

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