1N4Q

Protein Geranylgeranyltransferase type-I Complexed with a GGPP Analog and a KKKSKTKCVIL Peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structure of mammalian protein geranylgeranyltransferase type-I

Taylor, J.S., Reid, T.S., Terry, K.L., Casey, P.J., Beese, L.S.

(2003) EMBO J. 22: 5963-5974

  • DOI: 10.1093/emboj/cdg571
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Protein geranylgeranyltransferase type-I (GGTase-I), one of two CaaX prenyltransferases, is an essential enzyme in eukaryotes. GGTase-I catalyzes C-terminal lipidation of >100 proteins, including many GTP- binding regulatory proteins. We present the ...

    Protein geranylgeranyltransferase type-I (GGTase-I), one of two CaaX prenyltransferases, is an essential enzyme in eukaryotes. GGTase-I catalyzes C-terminal lipidation of >100 proteins, including many GTP- binding regulatory proteins. We present the first structural information for mammalian GGTase-I, including a series of substrate and product complexes that delineate the path of the chemical reaction. These structures reveal that all protein prenyltransferases share a common reaction mechanism and identify specific residues that play a dominant role in determining prenyl group specificity. This hypothesis was confirmed by converting farnesyltransferase (15-C prenyl substrate) into GGTase-I (20-C prenyl substrate) with a single point mutation. GGTase-I discriminates against farnesyl diphosphate (FPP) at the product turnover step through the inability of a 15-C FPP to displace the 20-C prenyl-peptide product. Understanding these key features of specificity is expected to contribute to optimization of anti-cancer and anti-parasite drugs.

    Organizational Affiliation: 

    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
A, C, E, G, I, K
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
Geranylgeranyl transferase type-1 subunit beta
B, D, F, H, J, L
377Rattus norvegicusMutation(s): 0 
Gene Names: Pggt1b
EC: 2.5.1.59
Find proteins for P53610 (Rattus norvegicus)
Go to UniProtKB:  P53610
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
M, N, O, P, Q, R
11Homo sapiensMutation(s): 0 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
B, D, F, H, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
C, D, F, G, H, J, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GER
Query on GER
Download SDF File 
Download CCD File 
R
GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
 Ligand Interaction
MGM
Query on MGM
Download SDF File 
Download CCD File 
B, D, F, H, J, L
2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
3-AZAGERANYLGERANYL DIPHOSPHATE
C19 H37 N O7 P2
OEMBPHBKZPOPBN-NWLVNBMCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 271.055α = 90.00
b = 268.033β = 131.73
c = 184.971γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Advisory, Database references, Source and taxonomy, Structure summary