2UUV

alkyldihydroxyacetonephosphate synthase in P1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Crucial Step in Ether Phospholipid Biosynthesis: Structural Basis of a Noncanonical Reaction Associated with a Peroxisomal Disorder.

Razeto, A.Mattiroli, F.Carpanelli, E.Aliverti, A.Pandini, V.Coda, A.Mattevi, A.

(2007) Structure 15: 683

  • DOI: 10.1016/j.str.2007.04.009
  • Primary Citation of Related Structures:  2UUU

  • PubMed Abstract: 
  • Ether phospholipids are essential constituents of eukaryotic cell membranes. Rhizomelic chondrodysplasia punctata type 3 is a severe peroxisomal disorder caused by inborn deficiency of alkyldihydroxyacetonephosphate synthase (ADPS). The enzyme carrie ...

    Ether phospholipids are essential constituents of eukaryotic cell membranes. Rhizomelic chondrodysplasia punctata type 3 is a severe peroxisomal disorder caused by inborn deficiency of alkyldihydroxyacetonephosphate synthase (ADPS). The enzyme carries out the most characteristic step in ether phospholipid biosynthesis: formation of the ether bond. The crystal structure of ADPS from Dictyostelium discoideum shows a fatty-alcohol molecule bound in a narrow hydrophobic tunnel, specific for aliphatic chains of 16 carbons. Access to the tunnel is controlled by a flexible loop and a gating helix at the protein-membrane interface. Structural and mutagenesis investigations identify a cluster of hydrophilic catalytic residues, including an essential tyrosine, possibly involved in substrate proton abstraction, and the arginine that is mutated in ADPS-deficient patients. We propose that ether bond formation might be orchestrated through a covalent imine intermediate with the flavin, accounting for the noncanonical employment of a flavin cofactor in a nonredox reaction.


    Organizational Affiliation

    Dipartimento di Genetica e Microbiologia, Università di Pavia, via Ferrata 1, 27100 Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE
A, B, C, D
584Dictyostelium discoideumGene Names: eapA
EC: 2.5.1.26
Find proteins for O96759 (Dictyostelium discoideum)
Go to UniProtKB:  O96759
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
PL3
Query on PL3

Download SDF File 
Download CCD File 
A, B, D
HEXADECAN-1-OL
C16 H34 O
BXWNKGSJHAJOGX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.226 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 77.800α = 114.00
b = 98.000β = 93.00
c = 107.000γ = 103.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
SHELXDphasing
SHELXEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance