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- PDB-4nke: The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophos... -

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Entry
Database: PDB / ID: 4nke
TitleThe effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates
ComponentsFarnesyl pyrophosphate synthase
KeywordsTRANSFERASE / Alpha-Helical Prenyltransferase / Isoprene Biosynthesis / Lipid Synthesis / Steroid Biosynthesis / Isoprenoid Pathway / Cholesterol Synthesis / Bisphosphonates
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / (2E,6E)-farnesyl diphosphate synthase / Cholesterol biosynthesis / farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / geranyltranstransferase activity / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Chem-RIS / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsTsoumpra, M.K. / Barnett, B.L. / Muniz, J.R.C. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Russell, R.G.G. / Oppermann, U. / Dunford, J.E.
CitationJournal: To be Published
Title: The effects of Lysine 200 and Phenylalanine 239 Farnesyl Pyrophosphate Synthase (FPPS) mutations on the catalytic activity, crystal structure and inhibition by nitrogen containing bisphosphonates
Authors: Tsoumpra, M.K. / Barnett, B.L. / Muniz, J.R.C. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Russell, R.G.G. / Oppermann, U. / Dunford, J.E.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.name / _chem_comp.pdbx_synonyms / _citation_author.name
Revision 1.2Sep 20, 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8258
Polymers43,0991
Non-polymers7267
Water7,278404
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,65016
Polymers86,1982
Non-polymers1,45314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8090 Å2
ΔGint-65 kcal/mol
Surface area27230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.260, 111.260, 66.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Farnesyl pyrophosphate synthase / FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / ...FPP synthase / FPS / (2E / 6E)-farnesyl diphosphate synthase / Dimethylallyltranstransferase / Farnesyl diphosphate synthase / Geranyltranstransferase


Mass: 43098.914 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: F239A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FDPS, FPS, KIAA1293 / Plasmid: PET 11 Derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase

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Non-polymers , 5 types, 411 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2
#4: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NH4Cl, PEG6000, 10% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 15, 2009
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.46→37.09 Å / Num. all: 72168 / Num. obs: 72107 / % possible obs: 99.3 % / Observed criterion σ(F): 2.1 / Observed criterion σ(I): 2.1 / Redundancy: 9.5 % / Biso Wilson estimate: 14.85 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 13.1
Reflection shellResolution: 1.46→1.54 Å / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP6

3cp6


Resolution: 1.46→32.39 Å / Cor.coef. Fo:Fc: 0.9518 / Cor.coef. Fo:Fc free: 0.9472 / SU R Cruickshank DPI: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1997 3636 5.04 %RANDOM
Rwork0.1798 ---
all0.1808 ---
obs0.1808 72107 99.19 %-
Displacement parametersBiso mean: 20.33 Å2
Baniso -1Baniso -2Baniso -3
1-1.2086 Å20 Å20 Å2
2--1.2086 Å20 Å2
3----2.4173 Å2
Refine analyzeLuzzati coordinate error obs: 0.169 Å
Refinement stepCycle: LAST / Resolution: 1.46→32.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 42 404 3158
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093073HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.874202HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1485SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes458HARMONIC5
X-RAY DIFFRACTIONt_it3073HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion2.52
X-RAY DIFFRACTIONt_chiral_improper_torsion382SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4251SEMIHARMONIC4
LS refinement shellResolution: 1.46→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2462 274 5.45 %
Rwork0.2328 4753 -
all0.2336 5027 -
obs--99.19 %
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)
11.3952-1.40560.11812.09240.47241.38090.0963-0.19040.02090.0575-0.06020.0469-0.3255-0.0982-0.0361-0.04610.0550.04390.0164-0.0094-0.0137-0.688430.12939.5651
21.49690.6038-0.5590.7236-0.16633.6422-0.0344-0.2241-0.03430.15510.00460.10290.0941-0.03770.0298-0.03370.00990.01310.0102-0.0104-0.045715.724925.746215.7311
32.15060.74640.12380.79380.18230.307-0.0405-0.2401-0.0474-0.030.01980.08320.0003-0.13740.0207-0.0417-0.0024-0.00070.04570.03060.0352-7.200924.90750.8693
41.02590.52350.07590.9176-0.12960.32490.0307-0.16310.08190.0816-0.02310.0528-0.0411-0.0324-0.0076-0.02610.0061-0.0054-0.0206-0.0047-0.014811.4529.79322.9338
53.03461.4647-0.18271.3439-0.24770.3840.0457-0.3039-0.11910.0229-0.0651-0.00470.0287-0.0720.0194-0.0148-0.0039-0.00440.00520.03130.008110.403517.86286.2783
61.48980.8598-0.69421.4712-1.03271.4469-0.02110.0141-0.0144-0.07780.03480.07760.0923-0.0008-0.0137-0.01840.0104-0.009-0.02810.00630.01113.120118.9906-8.602
72.21381.4252-0.75091.5442-0.98271.7535-0.07990.1526-0.0861-0.15350.0407-0.0470.12880.06250.0392-0.01580.0117-0.0159-0.0114-0.009-0.009216.886829.1324-18.7199
80.91280.43130.03930.6106-0.22880.4535-0.01250.04050.0228-0.08870.03410.08750.0453-0.0605-0.0216-0.0291-0.0042-0.0176-0.02650.00280.0092.282826.1947-12.9169
91.30020.24730.32650.37880.27790.338-0.030.21060.2381-0.06710.05460.0667-0.05440.0533-0.0247-0.0247-0.0124-0.0122-0.01320.05130.01415.061442.6014-19.7486
102.59660.1445-0.43990.0009-1.1070.39570.0086-0.0570.05690.05110.08870.0251-0.0343-0.0328-0.0973-0.0152-0.0061-0.0263-0.00660.00490.0056-6.615830.8105-11.7895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|9 - A|28 }A9 - 28
2X-RAY DIFFRACTION2{ A|29 - A|52 }A29 - 52
3X-RAY DIFFRACTION3{ A|53 - A|78 }A53 - 78
4X-RAY DIFFRACTION4{ A|79 - A|124 }A79 - 124
5X-RAY DIFFRACTION5{ A|125 - A|152 }A125 - 152
6X-RAY DIFFRACTION6{ A|153 - A|177 }A153 - 177
7X-RAY DIFFRACTION7{ A|178 - A|206 }A178 - 206
8X-RAY DIFFRACTION8{ A|207 - A|249 }A207 - 249
9X-RAY DIFFRACTION9{ A|250 - A|332 }A250 - 332
10X-RAY DIFFRACTION10{ A|333 - A|350 }A333 - 350

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