1N4Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.234 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGMClick on this verticalbar to view detailsBest fitted GERClick on this verticalbar to view details

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
  • Primary Citation of Related Structures:  
    1N4P, 1N4Q, 1N4R, 1N4S

  • 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
A, C, E, G, I
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
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, O, P, Q
11Homo sapiensMutation(s): 0 
EC: 3.6.5.2
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
MGM
Query on MGM

Download Ideal Coordinates CCD File 
AA [auth F]
EA [auth H]
HA [auth J]
KA [auth L]
T [auth B]
2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
C19 H37 N O7 P2
OEMBPHBKZPOPBN-NWLVNBMCSA-N
GER
Query on GER

Download Ideal Coordinates CCD File 
LA [auth R]GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
CA [auth H]
FA [auth J]
JA [auth L]
S [auth B]
V [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
BA [auth G]
DA [auth H]
GA [auth J]
IA [auth K]
U [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.234 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 271.055α = 90
b = 268.033β = 131.73
c = 184.971γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted MGMClick on this verticalbar to view detailsBest fitted GERClick on this verticalbar to view details

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: Advisory, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary