3KXC

Mutant transport protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Characterization of the self-palmitoylation activity of the transport protein particle component Bet3

Kummel, D.Walter, J.Heck, M.Heinemann, U.Veit, M.

(2010) Cell.Mol.Life Sci. 67: 2653-2664

  • DOI: 10.1007/s00018-010-0358-y

  • PubMed Abstract: 
  • Bet3, a transport protein particle component involved in vesicular trafficking, contains a hydrophobic tunnel occupied by a fatty acid linked to cysteine 68. We reported that Bet3 has a unique self-palmitoylating activity. Here we show that mutation ...

    Bet3, a transport protein particle component involved in vesicular trafficking, contains a hydrophobic tunnel occupied by a fatty acid linked to cysteine 68. We reported that Bet3 has a unique self-palmitoylating activity. Here we show that mutation of arginine 67 reduced self-palmitoylation of Bet3, but the effect was compensated by increasing the pH. Thus, arginine helps to deprotonate cysteine such that it could function as a nucleophile in the acylation reaction which is supported by the structural analysis of non-acylated Bet3. Using fluorescence spectroscopy we show that long-chain acyl-CoAs bind with micromolar affinity to Bet3, whereas shorter-chain acyl-CoAs do not interact. Mutants with a deleted acylation site or a blocked tunnel bind to Pal-CoA, only the latter with slightly reduced affinity. Bet3 contains three binding sites for Pal-CoA, but their number was reduced to two in the mutant with an obstructed tunnel, indicating that Bet3 contains binding sites on its surface.


    Organizational Affiliation

    Max Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trafficking protein particle complex subunit 3
A
194Homo sapiensMutation(s): 1 
Gene Names: TRAPPC3 (BET3)
Find proteins for O43617 (Homo sapiens)
Go to Gene View: TRAPPC3
Go to UniProtKB:  O43617
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Trafficking protein particle complex subunit 6B
C
158Homo sapiensMutation(s): 0 
Gene Names: TRAPPC6B
Find proteins for Q86SZ2 (Homo sapiens)
Go to Gene View: TRAPPC6B
Go to UniProtKB:  Q86SZ2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download SDF File 
Download CCD File 
A
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.172α = 90.00
b = 69.265β = 90.00
c = 121.376γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
HKL-2000data collection
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance