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- PDB-2h6g: W102T Protein Farnesyltransferase Mutant Complexed with a Geranyl... -

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Basic information

Entry
Database: PDB / ID: 2h6g
TitleW102T Protein Farnesyltransferase Mutant Complexed with a Geranylgeranylated DDPTASACVLS Peptide Product at 1.85A Resolution
Components
  • Protein farnesyltransferase beta subunit
  • Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
  • farnesylated peptide
KeywordsTRANSFERASE / FTase / farnesyltransferase / farnesyl transferase / prenyltransferase / CaaX / Ras / lipid modification / prenylation / substrate selectivity
Function / homology
Function and homology information


positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / positive regulation of tubulin deacetylation / protein farnesyltransferase ...positive regulation of deacetylase activity / skeletal muscle acetylcholine-gated channel clustering / protein geranylgeranyltransferase activity / peptide pheromone maturation / protein farnesylation / protein geranylgeranyltransferase type I / CAAX-protein geranylgeranyltransferase activity / CAAX-protein geranylgeranyltransferase complex / positive regulation of tubulin deacetylation / protein farnesyltransferase / protein farnesyltransferase activity / protein farnesyltransferase complex / Rab geranylgeranyltransferase activity / protein geranylgeranylation / positive regulation of skeletal muscle acetylcholine-gated channel clustering / microtubule associated complex / Apoptotic cleavage of cellular proteins / positive regulation of Rac protein signal transduction / alpha-tubulin binding / transforming growth factor beta receptor signaling pathway / lipid metabolic process / receptor tyrosine kinase binding / RAS processing / Inactivation, recovery and regulation of the phototransduction cascade / microtubule binding / molecular adaptor activity / Potential therapeutics for SARS / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid ...Protein farnesyltransferase subunit beta / Protein prenylyltransferase / Prenyltransferase subunit beta / Protein prenyltransferase, alpha subunit / Protein prenyltransferase alpha subunit repeat / Protein prenyltransferases alpha subunit repeat profile. / PFTB repeat / Prenyltransferase alpha-alpha toroid domain / Glycosyltransferase - #20 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
sucrose / GERAN-8-YL GERAN / Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha / Protein farnesyltransferase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsTerry, K.L. / Beese, L.S.
CitationJournal: Biochemistry / Year: 2006
Title: Conversion of protein farnesyltransferase to a geranylgeranyltransferase.
Authors: Terry, K.L. / Casey, P.J. / Beese, L.S.
History
DepositionMay 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit
B: Protein farnesyltransferase beta subunit
P: farnesylated peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3626
Polymers94,6803
Non-polymers6823
Water11,422634
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9050 Å2
ΔGint-61 kcal/mol
Surface area28830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.535, 178.535, 64.601
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit / CAAX farnesyltransferase alpha subunit / Ras proteins prenyltransferase alpha / FTase-alpha / Type ...CAAX farnesyltransferase alpha subunit / Ras proteins prenyltransferase alpha / FTase-alpha / Type I protein geranyl-geranyltransferase alpha subunit / GGTase-I-alpha


Mass: 44864.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Human FTase alpha subunit / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: P49354, protein farnesyltransferase, protein geranylgeranyltransferase type I
#2: Protein Protein farnesyltransferase beta subunit / CAAX farnesyltransferase beta subunit / RAS proteins prenyltransferase beta / FTase-beta


Mass: 48737.301 Da / Num. of mol.: 1 / Mutation: W102T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Human FTase beta subunit / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P49356, protein farnesyltransferase

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Protein/peptide / Sugars , 2 types, 2 molecules P

#3: Protein/peptide farnesylated peptide


Mass: 1078.152 Da / Num. of mol.: 1
Fragment: residues 173-180 of Rap2a, residues187-189 of H-Ras
Mutation: C176T, C177A / Source method: obtained synthetically / Details: Chemically synthesized
#4: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 636 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H34
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 14% PEG 8000, 200 mM ammonium acetate pH 5.2, 20 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2005 / Details: double mirror optics (MSC)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 103157 / Num. obs: 98678 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.071 / Net I/σ(I): 16.2
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.9 / Num. unique all: 9978 / Rsym value: 0.484 / % possible all: 97

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
CNSrefinement
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JCQ

1jcq


Resolution: 1.85→42.88 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4925 -Random
Rwork0.187 ---
obs0.187 98658 98.1 %-
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å21.6 Å20 Å2
2--1.18 Å20 Å2
3----2.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5932 0 44 634 6610
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.5
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.291 795 -
Rwork0.272 --
obs-16264 97.8 %

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