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- PDB-4q23: The role of threonine 201 and tyrosine 204 in the human farnesyl ... -

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Basic information

Entry
Database: PDB / ID: 4q23
TitleThe role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates
ComponentsFarnesyl pyrophosphate synthaseDimethylallyltranstransferase
KeywordsTRANSFERASE / ISOPRENE BIOSYNTHESIS / LIPID SYNTHESIS / STEROID BIOSYNTHESIS / ISOPRENOID PATHWAY / CHOLESTEROL SYNTHESIS / BISPHOSPHONATES / Alpha helical prenyltransferase / Isopentyl Pyrophosphate / Dimethylallyl Pyrophospahte
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
Chem-RIS / Farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsTsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Kwaasi, A.A. / Pilka, E.S. / Kavanagh, K.L. / Evdokimov, A. / Walter, R.L. / Ebetino, F.H. / von Delft, F. ...Tsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Kwaasi, A.A. / Pilka, E.S. / Kavanagh, K.L. / Evdokimov, A. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Oppermann, U. / Russell, R.G.G. / Dunford, J.E.
CitationJournal: To be Published
Title: The role of threonine 201 and tyrosine 204 in the human farnesyl pyrophosphate synthase catalytic mechanism and the mode of inhibition by the nitrogen-containing bisphosphonates
Authors: Tsoumpra, M.K. / Muniz, J.R.C. / Barnett, B.L. / Kwaasi, A.A. / Pilka, E.S. / Kavanagh, K.L. / Evdokimov, A. / Walter, R.L. / Ebetino, F.H. / von Delft, F. / Oppermann, U. / Russell, R.G.G. / Dunford, J.E.
History
DepositionApr 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: 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)43,5676
Polymers43,1151
Non-polymers4525
Water2,180121
1
A: Farnesyl pyrophosphate synthase
hetero molecules

A: Farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,13412
Polymers86,2302
Non-polymers90410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area6520 Å2
ΔGint-107 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.360, 111.360, 67.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 43114.957 Da / Num. of mol.: 1 / Fragment: UNP residues 67-419 / Mutation: T201A
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
#2: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate / Risedronic acid


Mass: 283.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H11NO7P2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NH4Cl, 20% PEG 6000, 10% 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: 1.98→25.02 Å / Num. all: 30003 / Num. obs: 29838 / % possible obs: 99.3 % / Observed criterion σ(F): 2.05 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.05 Å2
Reflection shellResolution: 1.98→2.05 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CP6

3cp6


Resolution: 1.98→25.02 Å / Cor.coef. Fo:Fc: 0.9507 / Cor.coef. Fo:Fc free: 0.9291 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 1512 5.07 %RANDOM
Rwork0.1915 ---
obs0.1931 29838 --
Displacement parametersBiso mean: 51.76 Å2
Baniso -1Baniso -2Baniso -3
1-5.4345 Å20 Å20 Å2
2--5.4345 Å20 Å2
3----10.869 Å2
Refine analyzeLuzzati coordinate error obs: 0.288 Å
Refinement stepCycle: LAST / Resolution: 1.98→25.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 0 25 121 2788
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012760HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933758HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1257SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes401HARMONIC5
X-RAY DIFFRACTIONt_it2760HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.78
X-RAY DIFFRACTIONt_other_torsion2.89
X-RAY DIFFRACTIONt_chiral_improper_torsion357SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3493SEMIHARMONIC4
LS refinement shellResolution: 1.98→2.05 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2728 147 5.06 %
Rwork0.2315 2761 -
all0.2336 2908 -
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)
10.3985-1.5641-1.13123.3141-1.53664.33250.10450.2020.2582-0.1763-0.1367-0.191-0.27060.34370.0322-0.2773-0.15180.13930.08330.05850.2114-0.87329.0744-25.9506
20.6539-2.7107-1.85930.39220.3213.5647-0.05610.4347-0.181-0.145-0.1724-0.2562-0.03160.25960.2286-0.139-0.04840.0926-0.0077-0.00230.1104-15.925927.9344-31.1703
32.72182.24492.3130.1888-1.88435.5334-0.04440.18950.1425-0.06390.146-0.1559-0.08830.5442-0.1016-0.2921-0.0827-0.0165-0.0747-0.08310.22533.847227.7589-15.0814
42.1279-0.3929-1.04330.61882.20180.11880.00980.02280.0236-0.0023-0.0328-0.04250.04370.05230.023-0.24370.00370.04560.2936-0.15020.30411.556218.9292-22.5258
52.507-0.18280.63341.18760.34261.34680.0060.1546-0.1166-0.06130.1143-0.1239-0.00980.1562-0.1203-0.1615-0.0194-0.0014-0.1554-0.01090.0944-13.931724.7999-16.7155
62.6001-1.29062.77258.16792.26332.80.1238-0.2565-0.31510.4850.0424-0.50280.1462-0.1831-0.1662-0.1785-0.0051-0.152-0.22660.04150.2433-17.003229.18862.2435
73.3187-0.6109-0.26033.38572.03014.80650.0737-0.022-0.35650.21280.0271-0.05840.29380.2764-0.1009-0.17990.0045-0.0907-0.0946-0.03840.26510.78219.7472-4.8659
82.5259-0.36690.13871.7670.14121.9872-0.1095-0.27880.48210.1920.1126-0.3368-0.26050.1031-0.0032-0.1047-0.0162-0.0789-0.1651-0.03410.1117-14.440640.1496-2.7291
91.73730.234-0.17981.3707-0.9794.0085-0.0376-0.54420.52070.54420.21840.1262-0.1697-0.1883-0.18070.00730.0854-0.0145-0.0053-0.10650.1031-25.791546.29156.2031
104.6088-2.1278-0.19963.74091.59031.9197-0.0648-0.14190.43540.0284-0.0592-0.1537-0.27380.02810.1241-0.1829-0.0444-0.0917-0.1098-0.05540.16410.39335.48832.5736
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|9 - 34}A9 - 34
2X-RAY DIFFRACTION2{A|35 - 55}A35 - 55
3X-RAY DIFFRACTION3{A|56 - 73}A56 - 73
4X-RAY DIFFRACTION4{A|74 - 83}A74 - 83
5X-RAY DIFFRACTION5{A|84 - 181}A84 - 181
6X-RAY DIFFRACTION6{A|182 - 205}A182 - 205
7X-RAY DIFFRACTION7{A|206 - 234}A206 - 234
8X-RAY DIFFRACTION8{A|235 - 273}A235 - 273
9X-RAY DIFFRACTION9{A|274 - 305}A274 - 305
10X-RAY DIFFRACTION10{A|306 - 349}A306 - 349

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