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- PDB-8ppd: Human inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic do... -

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Basic information

Entry
Database: PDB / ID: 8ppd
TitleHuman inositol 1,4,5-trisphosphate 3-kinase A (IP3K) catalytic domain in complex with DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate/ATP/Mn
ComponentsInositol-trisphosphate 3-kinase A
KeywordsTRANSFERASE / Inositol polyphosphate / InsP / inositol kinase / IP3K / calcium / InsP3 / IP3 / IPK / IP3 3-K
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / inositol metabolic process / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / calcium/calmodulin-dependent protein kinase activity / dendritic spine maintenance ...inositol-trisphosphate 3-kinase / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / inositol metabolic process / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / calcium/calmodulin-dependent protein kinase activity / dendritic spine maintenance / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol phosphate biosynthetic process / cellular response to calcium ion / response to calcium ion / regulation of synaptic plasticity / small GTPase binding / actin cytoskeleton organization / dendritic spine / cytoskeleton / calmodulin binding / glutamatergic synapse / signal transduction / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase
Similarity search - Domain/homology
: / ADENOSINE-5'-TRIPHOSPHATE / : / Inositol-trisphosphate 3-kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.77 Å
AuthorsMarquez-Monino, M.A. / Gonzalez, B.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-117400GB-100 Spain
Spanish Ministry of Economy and CompetitivenessBFU2017-89913-P Spain
CitationJournal: Nat Commun / Year: 2024
Title: Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity.
Authors: Marquez-Monino, M.A. / Ortega-Garcia, R. / Whitfield, H. / Riley, A.M. / Infantes, L. / Garrett, S.W. / Shipton, M.L. / Brearley, C.A. / Potter, B.V.L. / Gonzalez, B.
History
DepositionJul 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol-trisphosphate 3-kinase A
B: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,41915
Polymers63,7552
Non-polymers2,66513
Water5,152286
1
A: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1627
Polymers31,8771
Non-polymers1,2846
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inositol-trisphosphate 3-kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2588
Polymers31,8771
Non-polymers1,3807
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.160, 97.524, 192.056
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-503-

SO4

21B-717-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inositol-trisphosphate 3-kinase A / Inositol 1 / 4 / 5-trisphosphate 3-kinase A / IP3 3-kinase A / IP3K A / InsP 3-kinase A


Mass: 31877.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Catalytic domain / Source: (gene. exp.) Homo sapiens (human) / Gene: ITPKA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star
References: UniProt: P23677, inositol-trisphosphate 3-kinase

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Non-polymers , 5 types, 299 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-75I / DL-6-deoxy-6-hydroxy-methyl-scyllo-inositol 1,2,4-trisphosphate / [(1R,2S,3S,4R,5S,6R)-2-(hydroxymethyl)-3,5-bis(oxidanyl)-4,6-diphosphonooxy-cyclohexyl] dihydrogen phosphate


Mass: 434.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17O15P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.31 % / Description: Cube / Trapezoidal
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.83 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. ...Details: 0.83 M sodium citrate, 0.1M Tris pH 8.5 and 0.1 M NaCl. Protein:precipitant ratio 1:1. Protein concentration: 18 mg/ml. Protein buffer: 20 mM Tris pH 7.5, 50 mM ammonium sulfate and 2 mM DTT. Soaking 2h with 1.5 M lithium sulfate, 0.1 M Tris pH 8.5, 10 mM ligand, 3 mM ATP and 3 mM MnCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979178 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2021 / Details: KB mirrors, rectangular beam shape
RadiationMonochromator: Channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979178 Å / Relative weight: 1
ReflectionResolution: 1.77→48.01 Å / Num. obs: 66119 / % possible obs: 99.7 % / Redundancy: 11 % / Biso Wilson estimate: 30.204 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.024 / Net I/σ(I): 16
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3675 / CC1/2: 0.607 / Rpim(I) all: 0.427 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.77→47.31 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.003 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23047 3335 5 %RANDOM
Rwork0.20191 ---
obs0.20331 62730 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.839 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å20 Å2
2---0.09 Å20 Å2
3----1.09 Å2
Refinement stepCycle: 1 / Resolution: 1.77→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4230 0 149 286 4665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134547
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174129
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.6586165
X-RAY DIFFRACTIONr_angle_other_deg1.2931.5919552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.9720.109274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.25515787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0311553
X-RAY DIFFRACTIONr_chiral_restr0.0650.2564
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025007
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021029
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.694.0152135
X-RAY DIFFRACTIONr_mcbond_other2.6864.0132134
X-RAY DIFFRACTIONr_mcangle_it3.9495.9882667
X-RAY DIFFRACTIONr_mcangle_other3.9495.9892668
X-RAY DIFFRACTIONr_scbond_it3.1164.442412
X-RAY DIFFRACTIONr_scbond_other3.1064.4332407
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8986.5233493
X-RAY DIFFRACTIONr_long_range_B_refined7.46446.6075093
X-RAY DIFFRACTIONr_long_range_B_other7.43646.3815040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2083medium positional0.480.5
1264tight thermal3.560.5
2083medium thermal4.22
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 210 -
Rwork0.387 4555 -
obs--98.21 %

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