1TN6

Protein Farnesyltransferase Complexed with a Rap2a Peptide Substrate and a FPP Analog at 1.8A Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 

wwPDB Validation 3D Report Full Report



Literature

Crystallographic analysis of CaaX prenyltransferases complexed with substrates defines rules of protein substrate selectivity

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

(2004) J Mol Biol 343: 417-433

  • DOI: 10.1016/j.jmb.2004.08.056
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Post-translational modifications are essential for the proper function of many proteins in the cell. The attachment of an isoprenoid lipid (a process termed prenylation) by protein farnesyltransferase (FTase) or geranylgeranyltransferase type I (GGTa ...

    Post-translational modifications are essential for the proper function of many proteins in the cell. The attachment of an isoprenoid lipid (a process termed prenylation) by protein farnesyltransferase (FTase) or geranylgeranyltransferase type I (GGTase-I) is essential for the function of many signal transduction proteins involved in growth, differentiation, and oncogenesis. FTase and GGTase-I (also called the CaaX prenyltransferases) recognize protein substrates with a C-terminal tetrapeptide recognition motif called the Ca1a2X box. These enzymes possess distinct but overlapping protein substrate specificity that is determined primarily by the sequence identity of the Ca1a2X motif. To determine how the identity of the Ca1a2X motif residues and sequence upstream of this motif affect substrate binding, we have solved crystal structures of FTase and GGTase-I complexed with a total of eight cognate and cross-reactive substrate peptides, including those derived from the C termini of the oncoproteins K-Ras4B, H-Ras and TC21. These structures suggest that all peptide substrates adopt a common binding mode in the FTase and GGTase-I active site. Unexpectedly, while the X residue of the Ca1a2X motif binds in the same location for all GGTase-I substrates, the X residue of FTase substrates can bind in one of two different sites. Together, these structures outline a series of rules that govern substrate peptide selectivity; these rules were utilized to classify known protein substrates of CaaX prenyltransferases and to generate a list of hypothetical substrates within the human genome.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase alpha subunitA382Homo sapiensMutation(s): 0 
Gene Names: FNTA
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (UniProt)
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

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein farnesyltransferase beta subunitB437Homo sapiensMutation(s): 0 
Gene Names: FNTB
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
peptide derived from the C-terminus of Rap2aC11N/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
D
2 N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FII
Query on FII

Download CCD File 
B
[(3,7,11-TRIMETHYL-DODECA-2,6,10-TRIENYLOXYCARBAMOYL)-METHYL]-PHOSPHONIC ACID
C17 H30 N O5 P
JAOBYUCYSAOLHS-XGGJEREUSA-N
 Ligand Interaction
ZN
Query on ZN

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B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACY
Query on ACY

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A, B
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.179 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.474α = 90
b = 178.474β = 90
c = 64.697γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    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