3KSL

Structure of FPT bound to DATFP-DH-GPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis, properties, and applications of diazotrifluropropanoyl-containing photoactive analogs of farnesyl diphosphate containing modified linkages for enhanced stability.

Hovlid, M.L.Edelstein, R.L.Henry, O.Ochocki, J.DeGraw, A.Lenevich, S.Talbot, T.Young, V.G.Hruza, A.W.Lopez-Gallego, F.Labello, N.P.Strickland, C.L.Schmidt-Dannert, C.Distefano, M.D.

(2010) Chem.Biol.Drug Des. 75: 51-67

  • DOI: 10.1111/j.1747-0285.2009.00914.x

  • PubMed Abstract: 
  • Photoactive analogs of farnesyl diphosphate (FPP) are useful probes in studies of enzymes that employ this molecule as a substrate. Here, we describe the preparation and properties of two new FPP analogs that contain diazotrifluoropropanoyl photophor ...

    Photoactive analogs of farnesyl diphosphate (FPP) are useful probes in studies of enzymes that employ this molecule as a substrate. Here, we describe the preparation and properties of two new FPP analogs that contain diazotrifluoropropanoyl photophores linked to geranyl diphosphate via amide or ester linkages. The amide-linked analog (3) was synthesized in 32P-labeled form from geraniol in seven steps. Experiments with Saccharomyces cerevisiae protein farnesyltransferase (ScPFTase) showed that 3 is an alternative substrate for the enzyme. Photolysis experiments with [(32)P]3 demonstrate that this compound labels the beta-subunits of both farnesyltransferase and geranylgeranyltransferase (types 1 and 2). However, the amide-linked probe 3 undergoes a rearrangement to a photochemically unreactive isomeric triazolone upon long term storage making it inconvenient to use. To address this stability issue, the ester-linked analog 4 was prepared in six steps from geraniol. Computational analysis and X-ray crystallographic studies suggest that 4 binds to protein farnesyl transferase (PFTase) in a similar fashion as FPP. Compound 4 is also an alternative substrate for PFTase, and a 32P-labeled form selectively photocrosslinks the beta-subunit of ScPFTase as well as E. coli farnesyldiphosphate synthase and a germacrene-producing sesquiterpene synthase from Nostoc sp. strain PCC7120 (a cyanobacterial source). Finally, nearly exclusive labeling of ScPFTase in crude E. coli extract was observed, suggesting that [32P]4 manifests significant selectivity and should hence be useful for identifying novel FPP-utilizing enzymes in crude protein preparations.


    Organizational Affiliation

    Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyltransferase, CAAX box, alpha
A
377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.58, 2.5.1.59
Find proteins for Q04631 (Rattus norvegicus)
Go to UniProtKB:  Q04631
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase subunit beta
B
437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
Find proteins for Q02293 (Rattus norvegicus)
Go to UniProtKB:  Q02293
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SZH
Query on SZH

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Download CCD File 
B
(2S,6E)-8-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}-2,6-dimethyloct-6-en-1-yl (2S)-3,3,3-trifluoro-2-hydrazinopropanoate
C13 H25 F3 N2 O9 P2
KFWDKULCUAWZLX-NPZMFMJXSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SZHIC50: 30000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 171.191α = 90.00
b = 171.191β = 90.00
c = 69.217γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
StructureStudiodata collection
HKL-2000data scaling
BUSTERphasing
BUSTERrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance