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- PDB-9gr8: Crystal structure of the N-terminal kinase domain from Saccharomy... -

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Basic information

Entry
Database: PDB / ID: 9gr8
TitleCrystal structure of the N-terminal kinase domain from Saccharomyces cerevisiae Vip1 in complex with ADP.
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
KeywordsBIOSYNTHETIC PROTEIN / Inositol pyrophosphate / inositol pyrophosphate phosphatase / histidine acid phosphatase / phytase / enzyme mechanism / GAF domain / phosphate homeostasis
Function / homology
Function and homology information


inositol hexakisphosphate 4-kinase activity / inositol hexakisphosphate 6-kinase activity / inositol hexakisphosphate 3-kinase activity / regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / diphosphoinositol pentakisphosphate kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity ...inositol hexakisphosphate 4-kinase activity / inositol hexakisphosphate 6-kinase activity / inositol hexakisphosphate 3-kinase activity / regulation of bipolar cell growth / inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / diphosphoinositol pentakisphosphate kinase activity / diphosphoinositol-pentakisphosphate 1-kinase / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / inositol metabolic process / regulation of microtubule cytoskeleton organization / cytoskeleton / ATP binding / cytoplasm / cytosol
Similarity search - Function
Histidine acid phosphatase, VIP1 family / VIP1, N-terminal / Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain / ATP-grasp fold, RimK-type / RimK-like ATP-grasp domain / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsLee, K. / Raia, P. / Hothorn, M.
Funding support Switzerland, United States, 2items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_209412 Switzerland
Howard Hughes Medical Institute (HHMI)55008733 United States
CitationJournal: Nat Commun / Year: 2025
Title: A small signaling domain controls PPIP5K phosphatase activity in phosphate homeostasis.
Authors: Raia, P. / Lee, K. / Bartsch, S.M. / Rico-Resendiz, F. / Portugal-Calisto, D. / Vadas, O. / Panse, V.G. / Fiedler, D. / Hothorn, M.
History
DepositionSep 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3907
Polymers38,6521
Non-polymers7386
Water6,684371
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint5 kcal/mol
Surface area16400 Å2
Unit cell
Length a, b, c (Å)40.675, 83.172, 51.768
Angle α, β, γ (deg.)90.00, 94.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase / InsP6 and PP-IP5 kinase


Mass: 38652.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: VIP1, YLR410W / Cell line (production host): Tnao / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q06685, diphosphoinositol-pentakisphosphate 1-kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 23 % [v/v] PEG 3,350, 0.1 M citric acid / BIS-Tris propane pH 6.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000036 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000036 Å / Relative weight: 1
ReflectionResolution: 1.18→43.86 Å / Num. obs: 220120 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / CC1/2: 1 / Rrim(I) all: 0.104 / Net I/σ(I): 13.3
Reflection shellResolution: 1.18→1.25 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 36388 / CC1/2: 0.547 / Rrim(I) all: 2.02 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.18→43.86 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 10766 5 %
Rwork0.1526 --
obs0.1541 215318 96.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.18→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 47 371 3133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122974
X-RAY DIFFRACTIONf_angle_d1.2884039
X-RAY DIFFRACTIONf_dihedral_angle_d14.4241178
X-RAY DIFFRACTIONf_chiral_restr0.094431
X-RAY DIFFRACTIONf_plane_restr0.014525
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.190.35553050.34015884X-RAY DIFFRACTION83
1.19-1.210.35273230.33286130X-RAY DIFFRACTION87
1.21-1.220.33633330.32446403X-RAY DIFFRACTION90
1.22-1.240.31563350.29976465X-RAY DIFFRACTION91
1.24-1.250.30813450.29836466X-RAY DIFFRACTION92
1.25-1.270.30773460.28716650X-RAY DIFFRACTION94
1.27-1.290.32133490.28456669X-RAY DIFFRACTION94
1.29-1.310.29353550.26776811X-RAY DIFFRACTION95
1.31-1.330.30713580.25856814X-RAY DIFFRACTION97
1.33-1.350.263590.23956811X-RAY DIFFRACTION97
1.35-1.370.21783590.22016873X-RAY DIFFRACTION97
1.37-1.40.25633660.21666892X-RAY DIFFRACTION97
1.4-1.420.22653600.20476841X-RAY DIFFRACTION97
1.42-1.450.2373690.1896953X-RAY DIFFRACTION97
1.45-1.490.19923630.17876870X-RAY DIFFRACTION98
1.49-1.520.19893680.16376940X-RAY DIFFRACTION98
1.52-1.560.17563640.15956932X-RAY DIFFRACTION98
1.56-1.60.19573660.15266922X-RAY DIFFRACTION98
1.6-1.650.19333690.14326951X-RAY DIFFRACTION99
1.65-1.70.17443680.13476991X-RAY DIFFRACTION98
1.7-1.760.15863690.12987007X-RAY DIFFRACTION99
1.76-1.830.15533680.12066963X-RAY DIFFRACTION99
1.83-1.910.16563700.11427044X-RAY DIFFRACTION99
1.91-2.020.16733720.12117025X-RAY DIFFRACTION99
2.02-2.140.14813730.11177036X-RAY DIFFRACTION99
2.14-2.310.13913670.10976985X-RAY DIFFRACTION100
2.31-2.540.14993740.11977060X-RAY DIFFRACTION99
2.54-2.910.18753770.13387084X-RAY DIFFRACTION100
2.91-3.660.14443670.13577010X-RAY DIFFRACTION100
3.66-43.860.17033690.14597070X-RAY DIFFRACTION100

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