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- PDB-6k4g: Crystal structure of the PI5P4Kbeta-GMPPNP complex -

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Basic information

Entry
Database: PDB / ID: 6k4g
TitleCrystal structure of the PI5P4Kbeta-GMPPNP 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 / negative regulation of insulin receptor signaling pathway / autophagosome / regulation of autophagy / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cell surface receptor signaling pathway / 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-GUANYLATE ESTER / Phosphatidylinositol 5-phosphate 4-kinase type-2 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_restr_ncs / refine_ls_shell / reflns / software / struct_conf / struct_ncs_dom / struct_ncs_dom_lim / struct_sheet_range / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _pdbx_nonpoly_scheme.asym_id ..._cell.volume / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_restr.type / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _symmetry.space_group_name_Hall
Description: Real space R-factor / Provider: author / Type: Coordinate replacement
Revision 2.1May 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 2.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Mar 12, 2025Group: Database references / Refinement description / Structure summary
Category: pdbx_database_related / pdbx_entry_details / struct_ncs_dom_lim
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)91,4245
Polymers89,8582
Non-polymers1,5673
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-19 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.782, 184.625, 105.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 33 through 86 or (resid 87...
d_2ens_1(chain "B" and (resid 33 through 64 or (resid 65...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11VALVALASPASPAA33 - 14410 - 121
d_12ARGARGSERSERAA146 - 220123 - 197
d_13GLUGLUGLNGLNAA225 - 293202 - 270
d_14GLYGLYPROPROAA338 - 373315 - 350
d_15PROPROLEULEUAA400 - 415377 - 392
d_21VALVALASPASPBB33 - 14410 - 121
d_22ARGARGGLNGLNBB146 - 293123 - 270
d_23GLYGLYLEULEUBB338 - 415315 - 392

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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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion / 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: AR-NE3A / 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: 2.7→94.36 Å / Num. obs: 29724 / % possible obs: 99.3 % / Redundancy: 7.2 % / Biso Wilson estimate: 79.79 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 35.26
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 2.66 / Num. unique obs: 4406 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3X04

3x04


Resolution: 2.7→37.69 Å / SU ML: 0.4148 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.9787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2747 1486 5 %
Rwork0.223 28227 -
obs0.2255 29713 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→37.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4642 0 96 5 4743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914859
X-RAY DIFFRACTIONf_angle_d1.06346640
X-RAY DIFFRACTIONf_chiral_restr0.0569753
X-RAY DIFFRACTIONf_plane_restr0.0071852
X-RAY DIFFRACTIONf_dihedral_angle_d9.6464671
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 3.08682989883 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.790.40011340.35432538X-RAY DIFFRACTION99.89
2.79-2.890.37681350.32142555X-RAY DIFFRACTION99.89
2.89-30.34171330.30272534X-RAY DIFFRACTION100
3-3.140.29661350.28762566X-RAY DIFFRACTION99.96
3.14-3.30.30241340.26642547X-RAY DIFFRACTION100
3.3-3.510.32821350.24442567X-RAY DIFFRACTION100
3.51-3.780.29321360.22472581X-RAY DIFFRACTION100
3.78-4.160.25581350.2012574X-RAY DIFFRACTION100
4.16-4.760.26381370.18122596X-RAY DIFFRACTION100
4.76-60.22321380.20362620X-RAY DIFFRACTION99.96
6-37.690.2631340.21612549X-RAY DIFFRACTION93.55
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)
15.422690255061.845760004891.384237197574.644814298571.511568073565.913221510450.03302218412870.467235521195-0.0908005937211-0.1960272981680.365411206509-0.06724308239380.2002852121060.522777392013-0.3551789007730.4248416798120.01314390011020.06271885230920.4961550292670.03710276669320.43020026344843.042199746638.7522638458-12.4330602003
27.656333881761.533923743981.370981624126.783992744182.070696422885.93811593648-0.254014357903-0.07964937241550.392718608139-0.04675725410950.516464679316-0.1146922268-0.09910611518710.484872210692-0.2639602270310.4638342689280.03522180522050.05364075975090.56430007887-0.03267490359260.42649283634247.136276385448.714044732-5.60981668413
32.513511162080.7034556300310.9887491477945.174149003823.127676513925.04755669228-0.165385128341-0.09806333714770.747417833943-0.09445393969010.3111813503390.126625531012-0.6349829480570.50739696814-0.1484681012220.54388778995-0.116765084970.1129254343370.7042036894160.007830473929190.74493925897747.112236908761.5263649787-1.75237199086
44.25001383772-0.5629907369641.272943545513.250073335961.485037510751.14766873481-0.8515993704250.339934368891-0.731666572096-0.2411526286660.32794764442-0.262744488816-0.4280881322330.4978476829150.04031334769140.662617915799-0.2292499674690.1373967603821.1445441703-0.2744513351591.1127167942262.865079427160.73217001390.321642748178
56.15780421067-0.34237923283-0.5479564195375.873979727882.204505024846.81349104131-0.161910099343-0.7166874860170.953868935510.08275543749090.547325142312-0.222607686564-0.2438976711260.475344742949-0.363542447210.488990054997-0.002395475324540.004311413735860.650893862266-0.2424696482260.83545345632950.400669421362.94070460197.7044731256
69.042906172322.47849919478-1.313666331183.713687720550.2830933029664.821932150590.005160755129780.517922373343-0.234898852491-0.2966479076140.140568905081-0.0998365745823-0.05135738035560.118146915348-0.1756250641350.5419157177540.05693418834690.004340629999230.439697241329-0.04467774299990.40947190361435.031690363725.6003031453-17.0431133996
76.3745789483-0.2797320125754.565608352694.69040616279-4.324784641516.930751939770.3138512876760.0651874359901-0.3757681937190.392896860394-0.163820076579-0.04393443079210.5470086416970.723274434685-0.01152081208530.7864452874560.0447129815084-0.01917264822310.471337273626-0.00219194153130.72083146198536.737688875712.4772069672-13.946820875
82.96402501606-0.674069572921-0.5672662870883.946288682460.2458173014532.33325021815-0.110312060540.437902210833-0.755282190034-0.3876741979790.05606298384430.4410954783460.866480030336-0.08416274361890.08268728484470.88589898554-0.124215435464-0.07620339285540.678646105026-0.1856670794360.72448592047627.94636099594.95301928345-21.5210181453
90.936896720899-0.7510170585230.9664408404066.14244566625-3.004400406535.696055442940.6873239919060.134428894148-0.567539272375-1.17808746633-0.2505663776180.5805585938422.33052137465-0.458574702164-0.418925202581.26159126506-0.0975585478802-0.0869333196860.594106406428-0.0684836238481.1757976422725.3086502036-2.0624039569-14.4897995726
102.640273878570.785790226312-0.3093806004372.445080696411.166394373950.815395665440.2626445288780.498954739328-1.21060792429-0.303134843437-0.04195224967120.1811463926291.40048400192-0.1981093438670.06291314792051.64273028043-0.251613189026-0.3473449042420.777567471841-0.240405900861.2203806934222.2176752448-5.90340961105-19.1804000842
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 33 through 110 )AA33 - 1102 - 79
22chain 'A' and (resid 111 through 173 )AA111 - 17380 - 134
33chain 'A' and (resid 174 through 253 )AA174 - 253135 - 214
44chain 'A' and (resid 254 through 279 )AA254 - 279215 - 240
55chain 'A' and (resid 280 through 416 )AA280 - 416241 - 317
66chain 'B' and (resid 33 through 109 )BD33 - 1091 - 77
77chain 'B' and (resid 110 through 153 )BD110 - 15378 - 112
88chain 'B' and (resid 154 through 257 )BD154 - 257113 - 212
99chain 'B' and (resid 258 through 349 )BD258 - 349213 - 261
1010chain 'B' and (resid 350 through 415 )BD350 - 415262 - 301

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