2X8U

Sphingomonas wittichii Serine palmitoyltransferase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    2X8U

  • 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-ketodihydrosphingosine ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SERINE PALMITOYLTRANSFERASEA, B412Rhizorhabdus wittichii RW1Mutation(s): 0 
Gene Names: Swit_3900
EC: 2.3.1.50
UniProt
Find proteins for A5VD79 (Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273))
Explore A5VD79 
Go to UniProtKB:  A5VD79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5VD79
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLP
Query on PLP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.37α = 90
b = 99.37β = 90
c = 72.66γ = 120
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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