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- PDB-6pcl: Crystal structure of human diphosphoinositol polyphosphate phosph... -

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Basic information

Entry
Database: PDB / ID: 6pcl
TitleCrystal structure of human diphosphoinositol polyphosphate phosphohydrolase 1 in complex with 5-IP7
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 1
KeywordsHYDROLASE / inositol pyrophosphate / inositol phosphate / kinase / phosphatase / PPIP5K / cell polarity / osmotic response
Function / homology
Function and homology information


diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity ...diphosphoinositol polyphosphate catabolic process / inositol diphosphate pentakisphosphate diphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol diphosphate tetrakisphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase / diadenosine polyphosphate catabolic process / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol polyphosphate metabolic process / RNA decapping / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / Synthesis of pyrophosphates in the cytosol / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cell-cell signaling / manganese ion binding / magnesium ion binding / zinc ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-I7P / Diphosphoinositol polyphosphate phosphohydrolase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDollins, D.E. / Neubauer, J. / Dong, J. / York, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Vip1 is a kinase and pyrophosphatase switch that regulates inositol diphosphate signaling.
Authors: Dollins, D.E. / Bai, W. / Fridy, P.C. / Otto, J.C. / Neubauer, J.L. / Gattis, S.G. / Mehta, K.P.M. / York, J.D.
History
DepositionJun 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9997
Polymers17,1151
Non-polymers8846
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.560, 59.576, 62.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diphosphoinositol polyphosphate phosphohydrolase 1 / DIPP-1 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 1 / Nucleoside diphosphate-linked ...DIPP-1 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 1 / Nucleoside diphosphate-linked moiety X motif 3 / Nudix motif 3


Mass: 17115.367 Da / Num. of mol.: 1 / Fragment: residues 1-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT3, DIPP, DIPP1 / Production host: Escherichia coli (E. coli)
References: UniProt: O95989, diphosphoinositol-polyphosphate diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-I7P / (1r,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl trihydrogen diphosphate / 1D-myo-inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate


Mass: 740.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H19O27P7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.47 Å3/Da / Density % sol: 50.25 %
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 12 - 18% PEG 8000, 150 - 300 mM LiSO4, 0.1 M sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→27.6 Å / Num. obs: 40069 / % possible obs: 93.7 % / Redundancy: 12.5 % / Rsym value: 0.06 / Net I/σ(I): 58.2
Reflection shellResolution: 1.3→1.32 Å / Num. unique obs: 1363 / Rsym value: 0.365

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.4_6)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q9P

2q9p


Resolution: 1.3→27.6 Å / SU ML: 0.84 / Cross valid method: FREE R-VALUE / σ(F): 0.89 / Phase error: 13.86
RfactorNum. reflection% reflection
Rfree0.1609 1935 5.03 %
Rwork0.1429 --
obs0.1437 38468 89.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 60.252 Å2 / ksol: 0.455 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.2976 Å2-0 Å2-0 Å2
2---4.399 Å20 Å2
3----2.8986 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 45 162 1292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111238
X-RAY DIFFRACTIONf_angle_d1.3741708
X-RAY DIFFRACTIONf_dihedral_angle_d13.849514
X-RAY DIFFRACTIONf_chiral_restr0.087171
X-RAY DIFFRACTIONf_plane_restr0.007214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2957-1.3420.19191160.1782217X-RAY DIFFRACTION55
1.342-1.39570.19991580.15752975X-RAY DIFFRACTION74
1.3957-1.45920.16551910.14813364X-RAY DIFFRACTION83
1.4592-1.53610.15971870.13093678X-RAY DIFFRACTION92
1.5361-1.63240.14662200.12323898X-RAY DIFFRACTION96
1.6324-1.75840.14792000.12643963X-RAY DIFFRACTION98
1.7584-1.93530.14312230.12373973X-RAY DIFFRACTION98
1.9353-2.21520.14372110.11944085X-RAY DIFFRACTION100
2.2152-2.79050.14912360.13184094X-RAY DIFFRACTION100
2.7905-27.63080.17341930.15714286X-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)
10.233-0.02450.24770.77870.0670.6883-0.01750.03880.02430.1231-0.00750.0388-0.02030.0292-0.00770.08590.0079-0.02120.1211-0.00070.11324.38494.7717.4701
20.7408-0.43580.35540.99780.03861.2212-0.0111-0.00620.10530.05620.0374-0.1807-0.08560.169-0.01620.09340.0045-0.00920.1189-0.00520.12448.43759.750216.7565
30.2301-0.40380.07921.20350.05990.9271-0.0178-0.01250.08940.01140.0328-0.123-0.04370.1091-0.01570.0695-0.0051-0.00130.1022-0.00180.13925.22110.166715.5825
40.7423-0.6257-0.03760.92290.20690.35260.08310.1333-0.1014-0.2299-0.07350.0816-0.0491-0.02140.00540.13220.0203-0.00780.1451-0.00520.09973.23132.73074.379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 8:33)
2X-RAY DIFFRACTION2(chain A and resid 34:73)
3X-RAY DIFFRACTION3(chain A and resid 74:117)
4X-RAY DIFFRACTION4(chain A and resid 118:142)

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