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- PDB-7em4: Crystal structure of the PI5P4Kbeta F205L-ITP complex -

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Basic information

Entry
Database: PDB / ID: 7em4
TitleCrystal structure of the PI5P4Kbeta F205L-ITP complex
ComponentsPhosphatidylinositol 5-phosphate 4-kinase type-2 beta
KeywordsTRANSFERASE / Lipid Kinase / Phosphoinositide signaling
Function / homology
Function and homology information


1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process ...1-phosphatidylinositol-5-phosphate 4-kinase / 1-phosphatidylinositol-5-phosphate 4-kinase activity / 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate biosynthetic process / Synthesis of PIPs in the nucleus / 1-phosphatidylinositol-4-phosphate 5-kinase activity / autophagosome-lysosome fusion / positive regulation of autophagosome assembly / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / phosphatidylinositol phosphate biosynthetic process / autophagosome / negative regulation of insulin receptor signaling pathway / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / phosphorylation / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Phosphatidylinositol-4-phosphate 5-kinase / : / Phosphatidylinositol-4-phosphate 5-kinase, core / Phosphatidylinositol-4-phosphate 5-kinase, N-terminal / Phosphatidylinositol-4-phosphate 5-Kinase / Phosphatidylinositol phosphate kinase (PIPK) domain profile. / Phosphatidylinositol phosphate kinases
Similarity search - Domain/homology
Chem-CZU / INOSINE-5'-DIPHOSPHATE / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSenda, M. / Senda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
CitationJournal: Structure / Year: 2022
Title: The GTP responsiveness of PI5P4K beta evolved from a compromised trade-off between activity and specificity.
Authors: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / ...Authors: Takeuchi, K. / Ikeda, Y. / Senda, M. / Harada, A. / Okuwaki, K. / Fukuzawa, K. / Nakagawa, S. / Yu, H.Y. / Nagase, L. / Imai, M. / Sasaki, M. / Lo, Y.H. / Ito, D. / Osaka, N. / Fujii, Y. / Sasaki, A.T. / Senda, T.
History
DepositionApr 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
B: Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1545
Polymers89,7902
Non-polymers1,3653
Water181
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-22 kcal/mol
Surface area27980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.311, 185.530, 105.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Phosphatidylinositol 5-phosphate 4-kinase type-2 beta / 1-phosphatidylinositol 5-phosphate 4-kinase 2-beta / Diphosphoinositide kinase 2-beta / ...1-phosphatidylinositol 5-phosphate 4-kinase 2-beta / Diphosphoinositide kinase 2-beta / Phosphatidylinositol 5-phosphate 4-kinase type II beta / PI(5)P 4-kinase type II beta / PIP4KII-beta / PtdIns(5)P-4-kinase isoform 2-beta


Mass: 44894.887 Da / Num. of mol.: 2 / Mutation: F205L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIP4K2B, PIP5K2B / Production host: Escherichia coli (E. coli)
References: UniProt: P78356, 1-phosphatidylinositol-5-phosphate 4-kinase
#2: Chemical ChemComp-IDP / INOSINE-5'-DIPHOSPHATE


Mass: 428.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O11P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CZU / [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(6-oxidanylidene-1~{H}-purin-9-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / Inosine-5'-triphosphate / Inosine triphosphate


Mass: 508.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N4O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 9%(w/v) PEG4000, 0.1 M sodium citrate pH 6.0, 0.1 M magnesium acetate, 0.1 M lithium acetate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2018
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→48.55 Å / Num. obs: 26836 / % possible obs: 99.9 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 28.86
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3817 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K4H

6k4h


Resolution: 2.8→45.935 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2775 1341 5 %
Rwork0.2162 --
obs0.2193 26819 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→45.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4677 0 84 1 4762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094863
X-RAY DIFFRACTIONf_angle_d1.0966628
X-RAY DIFFRACTIONf_dihedral_angle_d7.4762936
X-RAY DIFFRACTIONf_chiral_restr0.055767
X-RAY DIFFRACTIONf_plane_restr0.006847
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.90010.43051320.32172512X-RAY DIFFRACTION100
2.9001-3.01620.36451320.29352505X-RAY DIFFRACTION100
3.0162-3.15340.38221320.27992517X-RAY DIFFRACTION100
3.1534-3.31970.30761330.2522519X-RAY DIFFRACTION100
3.3197-3.52760.26781330.23442534X-RAY DIFFRACTION100
3.5276-3.79980.2491340.20612533X-RAY DIFFRACTION100
3.7998-4.1820.25451340.18522544X-RAY DIFFRACTION100
4.182-4.78660.22071340.16682557X-RAY DIFFRACTION100
4.7866-6.02840.2591370.20552592X-RAY DIFFRACTION100
6.0284-45.9350.29661400.22932665X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.10222.82341.10314.65221.16787.13860.59780.1534-0.1719-0.3071-0.40871.5328-0.11340.03110.02260.4762-0.00060.10310.38340.03160.614536.8339.5121-9.4674
22.06992.26561.38914.83331.49265.6823-0.24290.1697-0.1027-0.33940.335-0.26160.25830.7268-0.15430.37790.12350.12440.476-0.01170.379846.18538.4439-14.0679
35.65812.4516-0.49713.05592.074.11040.0928-0.48730.46320.1021-0.10960.4224-0.04310.0303-0.13450.55340.04880.10140.4641-0.04880.466140.712647.5628-2.9398
43.5012-0.78490.39725.2263.02355.5914-0.20320.14840.63540.08080.6179-0.2148-0.48131.3141-0.2570.375-0.15330.08090.7459-0.02610.511550.94851.1773-7.5126
52.5635-0.32851.06715.34560.84436.3831-0.5091-0.17951.5566-0.25580.2150.396-1.23410.0844-0.01490.9275-0.01830.04510.81430.05591.001747.574272.77991.8606
65.25072.31891.48815.05872.34560.8868-0.3784-0.2818-0.02830.2670.1926-0.0552-0.0461-0.02460.20230.65970.02950.03910.7056-0.07430.536451.080860.21197.1862
75.41791.1429-2.83974.56250.3744.9042-0.1601-0.68491.3080.70530.0555-0.1145-1.0401-0.3351-0.25160.4167-0.087-0.01380.571-0.14560.921952.50363.26087.4147
85.0910.0747-2.8713.19022.66677.273-0.17361.63072.1577-2.03322.4138-1.5985-0.77141.0382-2.07150.9363-0.22740.20660.9396-0.31411.230761.069469.6243-0.33
93.37281.1456-0.01131.5635-0.22561.3950.05360.44750.0452-0.18450.1313-0.25890.11150.0649-0.15370.60520.08140.03850.5524-0.04890.501635.363325.6096-17.1061
106.34641.05872.1963.4674-1.09776.72650.08770.1253-0.45820.2902-0.15180.23940.66430.74380.28850.90420.0880.01950.4310.02450.654336.943412.5785-13.7656
114.2773-0.6179-0.34564.0194-0.26083.5040.06520.3016-0.2946-0.32310.17730.39210.6723-0.2272-0.13180.6637-0.1047-0.09260.4494-0.11940.463727.313612.6194-20.5506
123.5107-0.78992.94992.0744-2.08797.719-0.40550.7846-1.1695-0.7469-0.2113-0.59791.04532.2506-1.50422.3416-0.18350.03170.9354-0.47690.66128.606-7.8603-29.4274
132.1075-1.16590.86612.9467-0.95072.9720.42410.4525-0.8139-0.99770.02670.43162.0094-0.0798-0.42141.6285-0.1242-0.11550.6199-0.10641.112425.2968-5.1771-18.2804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 110 )
3X-RAY DIFFRACTION3chain 'A' and (resid 111 through 153 )
4X-RAY DIFFRACTION4chain 'A' and (resid 154 through 212 )
5X-RAY DIFFRACTION5chain 'A' and (resid 213 through 254 )
6X-RAY DIFFRACTION6chain 'A' and (resid 255 through 349 )
7X-RAY DIFFRACTION7chain 'A' and (resid 350 through 399 )
8X-RAY DIFFRACTION8chain 'A' and (resid 400 through 416 )
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 109 )
10X-RAY DIFFRACTION10chain 'B' and (resid 110 through 153 )
11X-RAY DIFFRACTION11chain 'B' and (resid 154 through 212 )
12X-RAY DIFFRACTION12chain 'B' and (resid 213 through 227 )
13X-RAY DIFFRACTION13chain 'B' and (resid 228 through 416 )

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