2X8U

Sphingomonas wittichii Serine palmitoyltransferase

• PDB DOI: https://doi.org/10.2210/pdb2X8U/pdb

• Classification: TRANSFERASE
• Organism(s): Rhizorhabdus wittichii RW1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-12 Released: 2010-03-23 
• Deposition Author(s): Raman, M.C.C., Johnson, K.A., Campopiano, D.J., Naismith, J.H.

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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 

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

• PubMed: 20578000 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.58 kDa 
• Atom Count: 6,558 
• Modelled Residue Count: 798 
• Deposited Residue Count: 824 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE PALMITOYLTRANSFERASE	A, B	412	Rhizorhabdus wittichii RW1	Mutation(s): 0  EC: 2.3.1.50

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	C [auth A], D [auth B]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N

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 = 99.37	α = 90
b = 99.37	β = 90
c = 72.66	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Raman, M.C.C., Johnson, K.A., Campopiano, D.J., Naismith, J.H.

Revision History  

• 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