2X8U

Sphingomonas wittichii Serine palmitoyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Serine Palmitoyltransferase from Sphingomonas Wittichii Rw1 an Interesting Link to an Unusual Acyl Carrier Protein

Raman, M.C.C.Johnson, K.A.Clarke, D.J.Naismith, J.H.Campopiano, D.J.

(2010) Biopolymers 93: 811

  • DOI: 10.1002/bip.21482

  • PubMed Abstract: 
  • Serine palmitoyltransferase (SPT) catalyses the first step in the de novo biosynthesis of sphingolipids (SLs). It uses a decarboxylative Claisen-like condensation reaction to couple L-serine with palmitoyl-CoA to generate a long-chain base product, 3 ...

    Serine palmitoyltransferase (SPT) catalyses the first step in the de novo biosynthesis of sphingolipids (SLs). It uses a decarboxylative Claisen-like condensation reaction to couple L-serine with palmitoyl-CoA to generate a long-chain base product, 3-ketodihydrosphingosine. SLs are produced by mammals, plants, yeast, and some bacteria, and we have exploited the complete genome sequence of Sphingomonas wittichii to begin a complete analysis of bacterial sphingolipid biosynthesis. Here, we describe the enzymatic characterization of the SPT from this organism and present its high-resolution x-ray structure. Moreover, we identified an open reading frame with high sequence homology to acyl carrier proteins (ACPs) that are common to fatty acid biosynthetic pathways. This small protein was co-expressed with the SPT and we isolated and characterised the apo- and holo-forms of the ACP. Our studies suggest a link between fatty acid and sphingolipid metabolism.


    Organizational Affiliation

    School of Chemistry, EaStCHEM, University of Edinburgh, West Mains Road, Edinburgh EH9 3JJ.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERINE PALMITOYLTRANSFERASE
A, B
412Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)Mutation(s): 0 
EC: 2.3.1.50
Find proteins for A5VD79 (Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273))
Go to UniProtKB:  A5VD79
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download SDF File 
Download CCD File 
A, B
PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 99.370α = 90.00
b = 99.370β = 90.00
c = 72.660γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2015-11-11
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary