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- PDB-7em6: Crystal structure of the PI5P4Kbeta N203D-ITP complex -

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Basic information

Entry
Database: PDB / ID: 7em6
TitleCrystal structure of the PI5P4Kbeta N203D-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 / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane ...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 / phosphatidylinositol phosphate biosynthetic process / PI5P Regulates TP53 Acetylation / Synthesis of PIPs at the plasma membrane / negative regulation of insulin receptor signaling pathway / autophagosome / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / regulation of autophagy / endoplasmic reticulum membrane / GTP binding / protein homodimerization activity / nucleoplasm / ATP binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Phosphatidylinositol Phosphate Kinase II Beta / Phosphatidylinositol Phosphate Kinase II Beta / 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 / 2-Layer Sandwich / Alpha Beta
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: 2.95 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)91,2245
Polymers89,8602
Non-polymers1,3653
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-22 kcal/mol
Surface area27580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.079, 186.438, 106.326
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: 44929.891 Da / Num. of mol.: 2 / Mutation: N203D
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


Mass: 508.166 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N4O14P3 / Feature type: SUBJECT OF INVESTIGATION
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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 9%(w/v) PEG4000, 0.1M sodium citrate pH 6.0, 0.1M magnesium acetate, 0.1M 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: 2.95→48.3 Å / Num. obs: 23179 / % possible obs: 99.9 % / Redundancy: 9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.52
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 2.71 / Num. unique obs: 3308 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6K4G

6k4g


Resolution: 2.95→35.687 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 1160 5 %
Rwork0.2139 --
obs0.2165 22934 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→35.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4633 0 85 0 4718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094822
X-RAY DIFFRACTIONf_angle_d1.1066578
X-RAY DIFFRACTIONf_dihedral_angle_d7.9652906
X-RAY DIFFRACTIONf_chiral_restr0.057763
X-RAY DIFFRACTIONf_plane_restr0.006839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.08420.37461440.31652722X-RAY DIFFRACTION100
3.0842-3.24670.41361420.29622702X-RAY DIFFRACTION100
3.2467-3.450.34521430.26322720X-RAY DIFFRACTION100
3.45-3.71610.27911440.22712731X-RAY DIFFRACTION100
3.7161-4.08960.23471440.20312735X-RAY DIFFRACTION100
4.0896-4.68020.24191450.17942758X-RAY DIFFRACTION100
4.6802-5.89230.2311460.19452773X-RAY DIFFRACTION100
5.8923-35.6870.26551520.21092878X-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)
14.28363.46051.97064.92541.82956.3169-0.03530.5678-0.1393-0.09720.2658-0.0430.39560.4312-0.14520.46830.06950.09860.47050.02720.483343.026539.189-12.6242
26.48620.9723-0.71633.59124.6517.095-0.3635-0.34520.43420.38840.27390.3827-0.2661-0.19320.06720.6662-0.00870.0540.48170.00770.588540.668447.8797-2.9831
32.438-0.83460.61625.93724.08665.9817-0.11550.16520.6628-0.01410.6309-0.2958-0.24841.0234-0.42220.4232-0.21720.04680.7801-0.01840.709750.242853.3379-6.5168
42.20182.1173-1.4552.7099-1.15825.76180.22090.32061.98880.28260.24010.9316-1.56870.3455-0.42851.0633-0.06280.0180.89960.08591.316646.934974.12941.3451
58.19841.02760.58465.74021.68834.0698-1.19220.3985-0.5046-0.09490.32530.01090.32720.27750.53610.6544-0.02560.06690.782-0.14560.616452.885162.39375.7168
65.71322.2063-0.70754.08791.94815.71280.035-0.01740.81240.24750.7359-0.6604-0.07740.3751-0.76010.5794-0.06680.06560.7103-0.26371.02953.764463.27845.2115
75.71223.1085-0.24672.7810.35863.5461-0.36440.4020.062-0.20510.4041-0.35050.24120.0035-0.05270.64940.06320.0430.4638-0.030.518235.01625.8593-17.0382
88.5111-0.10382.74724.7737-4.80116.394-0.01010.0568-0.5164-0.0998-0.50320.01861.33630.2740.52271.04830.06860.11580.5272-0.02430.724336.810412.9719-13.8299
94.601-0.5133-0.79964.9175-1.10715.398-0.10580.3681-0.329-0.45510.43670.4921.1171-0.2376-0.33540.7857-0.1816-0.06640.4607-0.14370.597127.30612.8502-20.6092
102.7488-0.01021.71115.1351-1.25593.54430.34750.8391-1.1003-0.9565-0.13380.27512.67650.1114-0.31721.7887-0.0306-0.04850.6775-0.20521.153425.1974-5.2866-19.8082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 110 )
2X-RAY DIFFRACTION2chain 'A' and (resid 111 through 153 )
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 217 )
4X-RAY DIFFRACTION4chain 'A' and (resid 218 through 253 )
5X-RAY DIFFRACTION5chain 'A' and (resid 254 through 300 )
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 416 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 109 )
8X-RAY DIFFRACTION8chain 'B' and (resid 110 through 153 )
9X-RAY DIFFRACTION9chain 'B' and (resid 154 through 212 )
10X-RAY DIFFRACTION10chain 'B' and (resid 213 through 416 )

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