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 
  • R-Value Work: 0.214 
  • R-Value Observed: 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:  
    1N4S, 1N4R, 1N4Q, 1N4P

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alphaA, C, E, G, I, K377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
Find proteins for Q04631 (Rattus norvegicus)
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Go to UniProtKB:  Q04631
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranyl transferase type-1 subunit betaB, D, F, H, J, L377Rattus norvegicusMutation(s): 0 
Gene Names: Pggt1b
EC: 2.5.1.59
Find proteins for P53610 (Rattus norvegicus)
Explore P53610 
Go to UniProtKB:  P53610
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fusion protein consisting of transforming protein p21b and Ras related protein Rap-2bM, N, O, P, Q, R11Homo sapiensMutation(s): 0 
Gene Names: KRAS, KRAS2, RASK2
EC: 3.6.5.2
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
NIH Common Fund Data Resources
PHAROS  P01116
GTEx  ENSG00000133703
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGM
Query on MGM
Download Ideal Coordinates CCD File 
B, D, F, H, J, L
2-[METHYL-(5-GERANYL-4-METHYL-PENT-3-ENYL)-AMINO]-ETHYL-DIPHOSPHATE
C19 H37 N O7 P2
OEMBPHBKZPOPBN-NWLVNBMCSA-N		 Ligand Interaction
GER
Query on GER
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R
GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N		 Ligand Interaction
ZN
Query on ZN
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B, D, F, H, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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C, D, F, G, H, J, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 
  • 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

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Entry History 

Deposition Data

Revision History 

  • 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