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- PDB-6k4h: Crystal structure of the PI5P4Kbeta-AMPPNP complex -

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Basic information

Entry
Database: PDB / ID: 6k4h
TitleCrystal structure of the PI5P4Kbeta-AMPPNP 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 Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / 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 Kinase Iibeta; Chain: A, domain 2 / 2-Layer Sandwich / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTakeuchi, K. / Senda, 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
DepositionMay 23, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Mar 12, 2025Group: Database references / Structure summary / Category: pdbx_database_related / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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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)91,3765
Polymers89,8582
Non-polymers1,5193
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-9 kcal/mol
Surface area29110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.637, 182.980, 105.999
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion
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: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 24, 2012
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→91.49 Å / Num. obs: 34195 / % possible obs: 98.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 77.66 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 43.63
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 2.45 / Num. unique obs: 5016

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X03

3x03


Resolution: 2.55→53.18 Å / SU ML: 0.3951 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.7671
RfactorNum. reflection% reflection
Rfree0.2819 1709 5 %
Rwork0.225 --
obs0.2278 34181 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 99.02 Å2
Refinement stepCycle: LAST / Resolution: 2.55→53.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4698 0 76 5 4779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814888
X-RAY DIFFRACTIONf_angle_d1.02056664
X-RAY DIFFRACTIONf_chiral_restr0.054772
X-RAY DIFFRACTIONf_plane_restr0.0067855
X-RAY DIFFRACTIONf_dihedral_angle_d4.41083349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.630.41071410.34932684X-RAY DIFFRACTION99.09
2.63-2.710.37811420.33962696X-RAY DIFFRACTION98.99
2.71-2.810.39651410.31932669X-RAY DIFFRACTION98.46
2.81-2.920.37631420.33582698X-RAY DIFFRACTION98.89
2.92-3.050.31931420.29342694X-RAY DIFFRACTION98.54
3.05-3.210.31511420.26852708X-RAY DIFFRACTION98.75
3.21-3.410.31771430.25782719X-RAY DIFFRACTION99.2
3.41-3.680.30241430.23762715X-RAY DIFFRACTION99.27
3.68-4.050.25631440.20522724X-RAY DIFFRACTION98.9
4.05-4.630.23761440.18292740X-RAY DIFFRACTION99.04
4.63-5.840.24811470.19072790X-RAY DIFFRACTION99.73
5.84-53.180.2841380.21742635X-RAY DIFFRACTION90.47
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)
16.321157791632.117410664151.759847592414.244045084641.502908852056.358921861980.1030454651750.02318160421940.001997786057820.07934407489510.2505275822890.195661394970.3296026566880.295684644245-0.330022038780.505205537530.04764370359030.08417271018820.4381392548960.04734977752720.41847710151141.78857689139.6366422482-10.4927607252
22.791467599521.802667414811.293600456676.447002327192.083135924834.9948591753-0.1317428741850.05079083643820.3250915305520.1162734497970.687762151036-0.472832674864-0.4048006701461.10456304706-0.5364301460670.520296562355-0.04196999942420.07871240337530.856834506752-0.1012982194180.5618499216250.83427400450.2741196084-7.80928402429
32.629907915810.6744549220611.924214831586.621175539444.421809140266.71535117184-0.42547217263-0.07276795777730.955907280993-0.2535816575950.3642610737190.287412348158-0.8656421761770.03729983272340.03331321417850.655165301067-0.01629103197260.08477806378580.7379735030530.05824124008690.84606128519445.152048207465.4667448354-0.45291202945
45.07364737805-0.5315639389022.417028399243.905880086611.293376052271.96781033974-0.55541775111.03280290674-0.326209347481-0.3563437586630.393988673146-0.751809814759-1.28263769201-0.0182315064580.1290967310820.650836476229-0.2205472477210.1204009245411.11656688129-0.2409427596680.99574515092262.551016605760.57944619930.265119199473
57.016137725010.381666524834-5.804751163214.95917639327-0.2811702179164.71919910316-0.559810509516-0.9494379062980.5137320580870.9804148366710.09103680916870.6547955134460.292275753427-0.41353436530.4750136943650.9480038405210.0696010419070.1340794878791.08123685778-0.3041823097650.88281060886837.081089975362.255740840714.3427048116
67.234680962984.22362747302-1.839446738366.927670882120.6722402712785.42582922813-0.315235243798-0.177357182361.025198511480.005130602263720.794087682711-0.59097246503-0.2946210402570.336319333627-0.47553007910.6651306608240.0350884170240.0190261204550.709175006277-0.2932729650260.9921517394253.602328606862.7228781276.02578982044
78.277539774431.89581390401-3.976975076723.094996956580.745190306995.86932810675-0.2115977290950.392929665091-0.071253467459-0.08576481965460.246354881506-0.2330946692090.2609209416790.103306494086-0.02155969570050.6120076345690.0233951271118-0.0208847313870.410476503117-0.01201633561110.43716184167733.63848426525.4121449874-16.4651298716
89.714894125545.80045085288-0.202590704345.6741114547-0.4676853960241.818565028860.1032171583790.197304937171-0.057178579894-0.4412974392770.0298742260157-0.208684178158-0.07495296429110.392246536084-0.1475350637070.6656418129960.05993720175180.073749137880.576648207019-0.08830076957550.52009232996736.410705300625.2266348108-18.430751724
96.97507751271-0.2292336106073.217882560084.15133967086-4.343582039366.030440662650.4822221346680.239919232633-0.733147920349-0.0484430266627-0.153880027047-0.3137201774750.9137490974770.139575072332-0.2483376279790.9539912607990.03279793062760.03605541904120.451349543627-0.09021762063850.88384945343536.730804475412.1952320166-14.1344724965
103.03042516579-0.159186015548-1.019499377845.06369212931-0.8940043123932.32345694293-0.00446113233370.600525223331-0.917325572509-0.4194275988820.07587843342620.5431189773371.07044963285-0.43181635362-0.04955111958481.01999281395-0.182543350786-0.1129423945460.646123646199-0.1947037295620.77731082852125.77434794664.99784760495-21.6335438582
111.81905344257-0.204389320406-0.2198575510612.8519426888-1.209633054141.183266012610.4507018809970.198692314111-0.84555519646-1.0990486365-0.1947091918420.009799097505861.536573263850.258963619239-0.32167665721.70383625912-0.0610336456473-0.07068549383240.562250028464-0.1016128255651.2390533151428.6885042081-4.35853930668-12.9252409908
129.684260550570.2635102684915.46332792030.274291362266-0.6016502567617.947280446231.07413170846-0.266007169886-0.0394067541448-2.31669494018-0.05547454459952.426818960660.660133382886-0.471696267205-0.8890251400082.16656433107-0.24093646188-0.4356458944771.1816873247-0.3090186318021.661513053216.3090760994-6.43690651694-25.8353532371
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 138 )
2X-RAY DIFFRACTION2chain 'A' and (resid 139 through 191 )
3X-RAY DIFFRACTION3chain 'A' and (resid 192 through 253 )
4X-RAY DIFFRACTION4chain 'A' and (resid 254 through 279 )
5X-RAY DIFFRACTION5chain 'A' and (resid 280 through 302 )
6X-RAY DIFFRACTION6chain 'A' and (resid 303 through 416 )
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 80 )
8X-RAY DIFFRACTION8chain 'B' and (resid 81 through 109 )
9X-RAY DIFFRACTION9chain 'B' and (resid 110 through 153 )
10X-RAY DIFFRACTION10chain 'B' and (resid 154 through 273 )
11X-RAY DIFFRACTION11chain 'B' and (resid 274 through 400 )
12X-RAY DIFFRACTION12chain 'B' and (resid 401 through 415 )

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