2IEJ

Human Protein Farnesyltransferase Complexed with Inhibitor Compound STN-48 And FPP Analog at 1.8A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation 3D Report Full Report



Literature

Resistance mutations at the lipid substrate binding site of Plasmodium falciparum protein farnesyltransferase.

Eastman, R.T.White, J.Hucke, O.Yokoyama, K.Verlinde, C.L.Hast, M.A.Beese, L.S.Gelb, M.H.Rathod, P.K.Van Voorhis, W.C.

(2007) Mol Biochem Parasitol 152: 66-71

  • DOI: 10.1016/j.molbiopara.2006.11.012
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The post-translational farnesylation of proteins serves to anchor a subset of intracellular proteins to membranes in eukaryotic organisms and also promotes protein-protein interactions. This enzymatic reaction is carried out by protein farnesyltransf ...

    The post-translational farnesylation of proteins serves to anchor a subset of intracellular proteins to membranes in eukaryotic organisms and also promotes protein-protein interactions. This enzymatic reaction is carried out by protein farnesyltransferase (PFT), which catalyzes the transfer of a 15-carbon isoprenoid lipid unit, a farnesyl group, from farnesyl pyrophosphate to the C-termini of proteins containing a CaaX motif. Inhibition of PFT is lethal to the pathogenic protozoa Plasmodium falciparum. Previously, we have shown that parasites resistant to a tetrahydroquinoline (THQ)-based PFT inhibitor BMS-388891 have mutations leading to amino acid substitutions in PFT that map to the peptide substrate binding domain. We now report the selection of parasites resistant to another THQ PFT inhibitor BMS-339941. In whole cell assays sensitivity to BMS-339941 was reduced by 33-fold in a resistant clone, and biochemical analysis demonstrated a corresponding 33-fold increase in the BMS-339941 K(i) for the mutant PFT enzyme. More detailed kinetic analysis revealed that the mutant enzyme required higher concentration of peptide and farnesyl pyrophosphate substrates for optimum catalysis. Unlike previously characterized parasites resistant to BMS-388891, the resistant parasites have a mutation which is predicted to be in a distinct location of the enzymatic pocket, near the farnesyl pyrophosphate binding pocket. This is the first description of a mutation from any species affecting the farnesyl pyrophosphate binding pocket with reduced efficacy of PFT inhibitors. These data provide further support that PFT is the target of THQ inhibitors in P. falciparum and suggest that PFT inhibitors should be combined with other antimalarial agents to minimize the development of resistant parasites.


    Organizational Affiliation

    Department of Pathobiology, University of Washington, Seattle, WA 98195-7185, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunitA382Homo sapiensMutation(s): 0 
Gene Names: FNTA
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
Find proteins for P49354 (Homo sapiens)
Explore P49354 
Go to UniProtKB:  P49354
NIH Common Fund Data Resources
PHAROS  P49354
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase subunit betaB437Homo sapiensMutation(s): 0 
Gene Names: FNTB
EC: 2.5.1.58
Find proteins for P49356 (Homo sapiens)
Explore P49356 
Go to UniProtKB:  P49356
NIH Common Fund Data Resources
PHAROS  P49356
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Oligosaccharides
Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2 N/A
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S48
Query on S48

Download CCD File 
B
METHYL N-{(3S)-1-[(1-METHYL-1H-IMIDAZOL-5-YL)METHYL]-6-PHENYL-1,2,3,4-TETRAHYDROQUINOLIN-3-YL}-N-[(1-METHYL-1H-IMIDAZOL-4-YL)SULFONYL]GLYCINATE
C27 H30 N6 O4 S
AXHJABJJHXFRSM-QHCPKHFHSA-N
 Ligand Interaction
FII
Query on FII

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B
[(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID
C17 H30 N O5 P
JAOBYUCYSAOLHS-XGGJEREUSA-N
 Ligand Interaction
ZN
Query on ZN

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B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.253α = 90
b = 178.253β = 90
c = 64.661γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary