2H6I

W102T/Y365F Protein Farnesyltransferase Double Mutant Complexed with a Geranylgeranylated DDPTASACVLS Peptide Product at 3.0A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 

wwPDB Validation 3D Report Full Report



Literature

Conversion of protein farnesyltransferase to a geranylgeranyltransferase.

Terry, K.L.Casey, P.J.Beese, L.S.

(2006) Biochemistry 45: 9746-9755

  • DOI: 10.1021/bi060295e
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Posttranslational modifications are essential for the proper function of a number of proteins in the cell. One such modification, the covalent attachment of a single isoprenoid lipid (prenylation), is carried out by the CaaX prenyltransferases, prote ...

    Posttranslational modifications are essential for the proper function of a number of proteins in the cell. One such modification, the covalent attachment of a single isoprenoid lipid (prenylation), is carried out by the CaaX prenyltransferases, protein farnesyltransferase (FTase) and protein geranylgeranyltransferase type-I (GGTase-I). Substrate proteins of these two enzymes are involved in a variety of cellular functions but are largely associated with signal transduction. These modified proteins include members of the Ras superfamily, heterotrimeric G-proteins, centromeric proteins, and a number of proteins involved in nuclear integrity. Although FTase and GGTase-I are highly homologous, they are quite selective for their substrates, particularly for their isoprenoid diphosphate substrates, FPP and GGPP, respectively. Here, we present both crystallographic and kinetic analyses of mutants designed to explore this isoprenoid specificity and demonstrate that this specificity is dependent upon two enzyme residues in the beta subunits of the enzymes, W102beta and Y365beta in FTase (T49beta and F324beta, respectively, in GGTase-I).


    Organizational Affiliation

    Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, 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: Human FTase alpha subunitFNTA
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 beta subunitB437Homo sapiensMutation(s): 2 
Gene Names: Human FTase beta subunitFNTB
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
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  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
farnesylated peptideP11N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2 N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GER
Query on GER

Download CCD File 
P
GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.270 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.126α = 90
b = 178.126β = 90
c = 64.904γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
HKL-2000data reduction
CNSrefinement
XDSdata reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    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