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- PDB-7em2: Crystal structure of the PI5P4Kbeta-XTP complex -

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Basic information

Entry
Database: PDB / ID: 7em2
TitleCrystal structure of the PI5P4Kbeta-XTP 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-CZC / Chem-CZF / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.1Apr 6, 2022Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.2May 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 1.3Jun 15, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 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)91,2705
Polymers89,8582
Non-polymers1,4133
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-11 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.848, 185.138, 105.810
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 / PIP4KII-beta / PtdIns(5)P-4-kinase isoform 2-beta


Mass: 44928.902 Da / Num. of mol.: 2
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-CZC / [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate / xanthosine diphosphate


Mass: 444.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O12P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CZF / [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate / xanthosine triphosphate


Mass: 524.165 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H15N4O15P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.04 Å3/Da / Density % sol: 59.6 %
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: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 22, 2018
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→70.47 Å / Num. obs: 33540 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 39.97
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 9 % / Rmerge(I) obs: 0.929 / Mean I/σ(I) obs: 2.88 / Num. unique obs: 4827 / % possible all: 99.9

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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: 3X04

3x04


Resolution: 2.6→38.103 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 1676 5 %
Rwork0.2196 --
obs0.2215 33522 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4640 0 88 7 4735
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094916
X-RAY DIFFRACTIONf_angle_d1.26729
X-RAY DIFFRACTIONf_dihedral_angle_d8.0373960
X-RAY DIFFRACTIONf_chiral_restr0.063774
X-RAY DIFFRACTIONf_plane_restr0.007854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67650.35871380.35222625X-RAY DIFFRACTION100
2.6765-2.76290.40811380.33092621X-RAY DIFFRACTION100
2.7629-2.86160.39381370.31532613X-RAY DIFFRACTION100
2.8616-2.97610.33761380.28952617X-RAY DIFFRACTION100
2.9761-3.11150.30171380.26712625X-RAY DIFFRACTION100
3.1115-3.27550.33951390.26612636X-RAY DIFFRACTION100
3.2755-3.48060.30051390.23832641X-RAY DIFFRACTION100
3.4806-3.74910.26311390.22022640X-RAY DIFFRACTION100
3.7491-4.1260.20841400.19222664X-RAY DIFFRACTION100
4.126-4.72210.20941410.17752676X-RAY DIFFRACTION100
4.7221-5.94570.24041420.19692690X-RAY DIFFRACTION100
5.9457-38.1030.24461470.21652798X-RAY DIFFRACTION100
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)
13.11130.05681.29387.88111.26017.14820.18820.10920.0356-0.333-0.06170.95430.1757-0.0377-0.0810.4826-0.04770.10370.48870.08740.555436.76739.1416-9.2269
22.56872.55221.47743.85060.61634.6428-0.17750.66-0.0495-0.35540.3817-0.27930.11610.7218-0.18450.42310.06780.10710.5589-0.02380.437546.054637.9609-14.3241
36.73810.65181.29166.1061.8417.0908-0.290.22880.34330.08920.4047-0.0513-0.3270.8526-0.07480.43860.01370.04090.5259-0.01720.386947.660948.3217-5.784
41.88710.45031.36124.8832.95955.2959-0.30330.13350.6437-0.03810.25370.3217-0.54070.1811-0.03630.4328-0.09610.08350.67920.08280.730345.900957.6414-3.9565
54.1658-0.09380.3137.53442.66221.6143-0.40210.09072.96920.4197-0.2786-0.0332-1.87690.77980.29930.9864-0.12530.09070.8491-0.08621.539350.637173.40065.7993
64.45730.43331.40093.28412.07683.6566-0.67340.2803-0.3170.25540.2921-0.2382-0.4065-0.05850.2280.555-0.11980.09780.5679-0.07990.713752.444361.67276.4633
74.6034-0.8251-1.98263.90870.06162.83590.2839-1.54551.53540.5295-0.3878-0.90720.18981.0065-0.27950.68210.04730.0310.857-0.37830.859849.608858.237415.1307
87.2755-0.0788-0.11648.43243.83169.1909-0.41110.28991.4919-0.90010.8408-0.1498-0.75171.7338-0.54170.5756-0.14480.02850.8029-0.13371.039557.767265.5043-1.1561
97.36561.9964-1.14333.33540.22874.52390.07050.6976-0.1026-0.27230.175-0.25380.12750.2863-0.23950.48420.05160.03320.410.00230.388435.174225.4869-17.0009
108.5944-1.10541.50924.1206-1.35976.2572-0.09880.5608-0.2772-0.03530.0379-0.03120.70790.2711-0.02040.7164-0.0416-0.03370.3152-0.0780.511530.329513.7106-17.4602
112.69640.2707-1.37334.9082-0.94332.9184-0.12840.6126-0.9163-0.53950.25710.10971.26770.2591-0.13491.0391-0.0037-0.17220.6566-0.23740.71131.24052.1373-21.617
121.0149-1.2141-0.09424.9666-0.83292.82430.7969-0.0998-0.6964-1.2339-0.18510.43562.4715-0.4534-0.37351.3396-0.1274-0.1440.5441-0.00381.144824.383-2.2694-13.8852
131.86640.3047-0.88964.63520.24690.45820.25520.3488-0.9545-0.7323-0.0852-0.00181.7757-0.4723-0.10541.7442-0.2227-0.39790.5947-0.20811.156321.9531-5.2135-19.7488
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 59 )
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 109 )
3X-RAY DIFFRACTION3chain 'A' and (resid 110 through 173 )
4X-RAY DIFFRACTION4chain 'A' and (resid 174 through 236 )
5X-RAY DIFFRACTION5chain 'A' and (resid 237 through 253 )
6X-RAY DIFFRACTION6chain 'A' and (resid 254 through 300 )
7X-RAY DIFFRACTION7chain 'A' and (resid 301 through 360 )
8X-RAY DIFFRACTION8chain 'A' and (resid 361 through 416 )
9X-RAY DIFFRACTION9chain 'B' and (resid 33 through 109 )
10X-RAY DIFFRACTION10chain 'B' and (resid 110 through 173 )
11X-RAY DIFFRACTION11chain 'B' and (resid 174 through 252 )
12X-RAY DIFFRACTION12chain 'B' and (resid 253 through 349 )
13X-RAY DIFFRACTION13chain 'B' and (resid 350 through 415 )

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