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Structure paper

TitleBiochemical and structural characterization of an inositol pyrophosphate kinase from a giant virus.
Journal, issue, pagesEmbo J., Vol. 43, Page 462-480, Year 2024
Publish dateJun 23, 2023 (structure data deposition date)
AuthorsZong, G. / Desfougeres, Y. / Portela-Torres, P. / Kwon, Y.U. / Saiardi, A. / Shears, S.B. / Wang, H.
External linksEmbo J. / PubMed:38216735
MethodsX-ray diffraction
Resolution1.3 - 2.61 Å
Structure data

PDB-8t8u:
Crystal structure of Terrestrivirus full-length Inositol pyrophosphate kinase in complex with ADP
Method: X-RAY DIFFRACTION / Resolution: 2.01 Å

PDB-8t8v:
Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with ADP
Method: X-RAY DIFFRACTION / Resolution: 1.96 Å

PDB-8t8w:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ATP
Method: X-RAY DIFFRACTION / Resolution: 2 Å

PDB-8t8x:
Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with AMP-PNP
Method: X-RAY DIFFRACTION / Resolution: 2.59 Å

PDB-8t8y:
Crystal structure of Terrestrivirus inositol pyrophosphate kinase in complex with ADP and 1,4,5-InsP3
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

PDB-8t8z:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-(1OH)IP5
Method: X-RAY DIFFRACTION / Resolution: 2.6 Å

PDB-8t90:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-(3OH)IP5
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8t91:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-IP6
Method: X-RAY DIFFRACTION / Resolution: 2.56 Å

PDB-8t92:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-D-(1,2,3,4)-IP4
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

PDB-8t93:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-L-(1,2,3,4)-IP4
Method: X-RAY DIFFRACTION / Resolution: 1.95 Å

PDB-8t95:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-(1,2,4,5)-IP4
Method: X-RAY DIFFRACTION / Resolution: 2.61 Å

PDB-8t96:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-IP5
Method: X-RAY DIFFRACTION / Resolution: 2.36 Å

PDB-8t97:
Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-IP6
Method: X-RAY DIFFRACTION / Resolution: 2.46 Å

PDB-8t98:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with Scyllo-3-PP-(1,2,4,5)IP4, Mg, and Fluoride ion
Method: X-RAY DIFFRACTION / Resolution: 1.3 Å

PDB-8t99:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with Scyllo-L-1,4-[PP]2-(2,3)IP2, Mg, and Fluoride ion
Method: X-RAY DIFFRACTION / Resolution: 1.5 Å

PDB-8tf9:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-IP7, produced upon myo-IP6 phosphorylation by TvI
Method: X-RAY DIFFRACTION / Resolution: 1.55 Å

PDB-8tfa:
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with myo-5-PP-IP4, produced upon myo-(2OH)-IP5 phosphorylation by TvIPK
Method: X-RAY DIFFRACTION / Resolution: 1.4 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HOH:
WATER

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-CD:
Unknown entry

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-I3P:
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE

ChemComp-ZNU:
(1S,2R,3S,4S,5S,6S)-6-hydroxycyclohexane-1,2,3,4,5-pentayl pentakis[dihydrogen (phosphate)]

ChemComp-ZNZ:
(1R,2R,3R,4S,5R,6R)-6-hydroxycyclohexane-1,2,3,4,5-pentayl pentakis[dihydrogen (phosphate)]

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

ChemComp-XID:
(1S,2R,3R,4S,5R,6R)-5,6-dihydroxycyclohexane-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)]

ChemComp-ZNQ:
(1R,2S,3S,4R,5S,6S)-5,6-dihydroxycyclohexane-1,2,3,4-tetrayl tetrakis[dihydrogen (phosphate)]

ChemComp-I4P:
(1S,3R,4R,6S)-1,3,4,6-TETRAPKISPHOSPHATE

ChemComp-K7V:
neo-Inositol pentakisphosphate

ChemComp-KGN:
D-chiro inositol hexakisphosphate

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

ChemComp-CL:
Unknown entry

ChemComp-F:
FLUORIDE ION

ChemComp-ZOW:
(1R,2S,3S,4R,5S,6S)-2,3-dihydroxy-5,6-bis(phosphonooxy)cyclohexane-1,4-diyl bis[trihydrogen (diphosphate)]

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

Source
  • terrestrivirus sp.
  • homo sapiens (human)
KeywordsVIRAL PROTEIN / Virus / Kinase / inositol phosphate / soil / myo-inositol / Terrestrivirus / HYDROLASE / inositol / phosphatase / NUT3 / DIPP1

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