4BBY

MAMMALIAN ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE: WILD-TYPE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Precursor of Ether Phospholipids is Synthesized by a Flavoenzyme Through Covalent Catalysis.

Nenci, S.Piano, V.Rosati, S.Aliverti, A.Pandini, V.Fraaije, M.W.Heck, A.J.R.Edmondson, D.E.Mattevi, A.

(2012) Proc Natl Acad Sci U S A 109: 18791

  • DOI: 10.1073/pnas.1215128109
  • Primary Citation of Related Structures:  
    4BCA, 4BC7, 4BC9, 4BBY

  • PubMed Abstract: 
  • The precursor of the essential ether phospholipids is synthesized by a peroxisomal enzyme that uses a flavin cofactor to catalyze a reaction that does not alter the redox state of the substrates. The enzyme crystal structure reveals a V-shaped active ...

    The precursor of the essential ether phospholipids is synthesized by a peroxisomal enzyme that uses a flavin cofactor to catalyze a reaction that does not alter the redox state of the substrates. The enzyme crystal structure reveals a V-shaped active site with a narrow constriction in front of the prosthetic group. Mutations causing inborn ether phospholipid deficiency, a very severe genetic disease, target residues that are part of the catalytic center. Biochemical analysis using substrate and flavin analogs, absorbance spectroscopy, mutagenesis, and mass spectrometry provide compelling evidence supporting an unusual mechanism of covalent catalysis. The flavin functions as a chemical trap that promotes exchange of an acyl with an alkyl group, generating the characteristic ether bond. Structural comparisons show that the covalent versus noncovalent mechanistic distinction in flavoenzyme catalysis and evolution relies on subtle factors rather than on gross modifications of the cofactor environment.


    Organizational Affiliation

    Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE, PEROXISOMALABCD658Cavia porcellusMutation(s): 0 
Gene Names: AGPS
EC: 2.5.1.26
Find proteins for P97275 (Cavia porcellus)
Explore P97275 
Go to UniProtKB:  P97275
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.295α = 90.43
b = 99.17β = 92.18
c = 107.835γ = 94.92
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2012-11-28
    Changes: Database references