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

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Basic information

Entry
Database: PDB / ID: 4ogu
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 synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / All Alpha-Helical / Prenyltransferase / Isoprene Biosynthesis / Lipid Biosynthesis / Steroid Biosynthesis / Isoprenoid Pathway / Cholesterol Synthesis
Function / homology
Function and homology information


geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding ...geranyl diphosphate biosynthetic process / dimethylallyltranstransferase / farnesyl diphosphate biosynthetic process / (2E,6E)-farnesyl diphosphate synthase / geranyltranstransferase activity / dimethylallyltranstransferase activity / Cholesterol biosynthesis / cholesterol biosynthetic process / Activation of gene expression by SREBF (SREBP) / RNA binding / nucleoplasm / metal ion binding / cytosol / cytoplasm
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
PAMIDRONATE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _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.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)43,6536
Polymers43,0991
Non-polymers5545
Water1,964109
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,30612
Polymers86,1982
Non-polymers1,10810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7040 Å2
ΔGint-75 kcal/mol
Surface area26140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.210, 111.210, 67.270
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-607-

HOH

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Components

#1: Protein Farnesyl pyrophosphate synthase / Dimethylallyltranstransferase / 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 (DE)
References: UniProt: P14324, (2E,6E)-farnesyl diphosphate synthase, dimethylallyltranstransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-IPE / 3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE / ISOPENTENYL PYROPHOSPHATE / Isopentenyl pyrophosphate


Mass: 246.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O7P2
#4: Chemical ChemComp-210 / PAMIDRONATE / (3-AMINO-1-HYDROXY-1-PHOSPHONO-PROPYL)PHOSPHONIC ACID / Pamidronic acid


Mass: 235.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H11NO7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M NH4Cl, PEG 6000, 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: 2.1→51.12 Å / Num. all: 25182 / Num. obs: 25116 / % possible obs: 99.9 % / Observed criterion σ(F): 2.7 / Observed criterion σ(I): 2.7 / Redundancy: 10.6 % / Biso Wilson estimate: 41.24 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.21 Å / % possible all: 100

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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: 2.1→24.4 Å / Cor.coef. Fo:Fc: 0.9512 / Cor.coef. Fo:Fc free: 0.9331 / SU R Cruickshank DPI: 0.187 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1284 5.11 %RANDOM
Rwork0.1973 ---
all0.199 25182 --
obs0.199 25116 99.83 %-
Displacement parametersBiso mean: 60.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.5758 Å20 Å20 Å2
2--1.5758 Å20 Å2
3----3.1516 Å2
Refine analyzeLuzzati coordinate error obs: 0.355 Å
Refinement stepCycle: LAST / Resolution: 2.1→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 30 109 2775
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012769HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.963776HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1293SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes402HARMONIC5
X-RAY DIFFRACTIONt_it2769HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_chiral_improper_torsion359SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3474SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2748 138 4.97 %
Rwork0.233 2638 -
all0.2351 2776 -
obs--99.83 %
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)
12.00681.51040.53343.8177-0.63671.03370.05-0.0877-0.01110.0341-0.1280.1506-0.1297-0.34250.078-0.30320.1520.152-0.0909-0.09050.2375-0.451230.44398.4617
22.31371.65110.09260.6002-0.45424.6370.0015-0.19580.02950.2307-0.05450.10890.0935-0.09670.0529-0.22270.09110.1011-0.1946-0.03690.30416.00825.769115.9039
35.1811-1.92181.5270.65360.92462.61430.01370.0135-0.06380.2207-0.02720.1954-0.0083-0.48060.0135-0.3040.10040.06060.03830.00290.304-5.30526.08470.1502
43.0634-0.05460.73552.78460.83152.238-0.0177-0.3966-0.12260.12340.01220.1183-0.1424-0.37840.0055-0.3040.07290.0474-0.2608-0.00710.303711.235125.37054.0537
53.21730.2622-0.77451.978-1.56542.6717-0.01210.319-0.1208-0.30160.01570.25080.1755-0.0598-0.0037-0.3040.0627-0.0448-0.1615-0.03580.30415.072424.51-13.862
64.13720.46950.12311.89820.28331.0633-0.04670.53720.2931-0.40660.0260.1989-0.1716-0.01190.0207-0.3040.0457-0.0513-0.1391-0.01070.30412.114334.8176-16.2734
74.0158-0.60650.00912.32230.33271.26880.18160.25180.4017-0.4163-0.3370.3262-0.2527-0.10780.1554-0.3040.0918-0.0893-0.1343-0.05750.3042.942437.9296-18.917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|8 - 28}A8 - 28
2X-RAY DIFFRACTION2{A|29 - 52}A29 - 52
3X-RAY DIFFRACTION3{A|53 - 78}A53 - 78
4X-RAY DIFFRACTION4{A|79 - 152}A79 - 152
5X-RAY DIFFRACTION5{A|153 - 206}A153 - 206
6X-RAY DIFFRACTION6{A|207 - 294}A207 - 294
7X-RAY DIFFRACTION7{A|295 - 350}A295 - 350

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