1N4P

Protein Geranylgeranyltransferase type-I Complexed with Geranylgeranyl Diphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1093/emboj/cdg571

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
A, C, E, G, I
A, C, E, G, I, K
377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-1 subunit beta
B, D, F, H, J
B, D, F, H, J, L
377Rattus norvegicusMutation(s): 0 
Gene Names: Pggt1b
EC: 2.5.1.59
UniProt
Find proteins for P53610 (Rattus norvegicus)
Explore P53610 
Go to UniProtKB:  P53610
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UniProt GroupP53610
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2b
M, N
11Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
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UniProt GroupP01116
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GRG
Query on GRG

Download Ideal Coordinates CCD File 
BA [auth H]
EA [auth J]
IA [auth L]
Q [auth B]
U [auth D]
BA [auth H],
EA [auth J],
IA [auth L],
Q [auth B],
U [auth D],
X [auth F]
GERANYLGERANYL DIPHOSPHATE
C20 H36 O7 P2
OINNEUNVOZHBOX-QIRCYJPOSA-N
GER
Query on GER

Download Ideal Coordinates CCD File 
JA [auth M],
KA [auth N]
GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
ZN
Query on ZN

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CA [auth J]
GA [auth L]
O [auth B]
S [auth D]
V [auth F]
CA [auth J],
GA [auth L],
O [auth B],
S [auth D],
V [auth F],
Z [auth H]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth H]
DA [auth J]
FA [auth K]
HA [auth L]
P [auth B]
AA [auth H],
DA [auth J],
FA [auth K],
HA [auth L],
P [auth B],
R [auth C],
T [auth D],
W [auth F],
Y [auth G]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 272.338α = 90
b = 271.566β = 131.56
c = 185.425γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations