5D91

Structure of a phosphatidylinositolphosphate (PIP) synthase from Renibacterium Salmoninarum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for phosphatidylinositol-phosphate biosynthesis.

Clarke, O.B.Tomasek, D.Jorge, C.D.Dufrisne, M.B.Kim, M.Banerjee, S.Rajashankar, K.R.Shapiro, L.Hendrickson, W.A.Santos, H.Mancia, F.

(2015) Nat Commun 6: 8505-8505

  • DOI: https://doi.org/10.1038/ncomms9505
  • Primary Citation of Related Structures:  
    5D91, 5D92

  • PubMed Abstract: 

    Phosphatidylinositol is critical for intracellular signalling and anchoring of carbohydrates and proteins to outer cellular membranes. The defining step in phosphatidylinositol biosynthesis is catalysed by CDP-alcohol phosphotransferases, transmembrane enzymes that use CDP-diacylglycerol as donor substrate for this reaction, and either inositol in eukaryotes or inositol phosphate in prokaryotes as the acceptor alcohol. Here we report the structures of a related enzyme, the phosphatidylinositol-phosphate synthase from Renibacterium salmoninarum, with and without bound CDP-diacylglycerol to 3.6 and 2.5 Å resolution, respectively. These structures reveal the location of the acceptor site, and the molecular determinants of substrate specificity and catalysis. Functional characterization of the 40%-identical ortholog from Mycobacterium tuberculosis, a potential target for the development of novel anti-tuberculosis drugs, supports the proposed mechanism of substrate binding and catalysis. This work therefore provides a structural and functional framework to understand the mechanism of phosphatidylinositol-phosphate biosynthesis.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AF2299 protein,Phosphatidylinositol synthase336Archaeoglobus fulgidus DSM 4304Renibacterium salmoninarum ATCC 33209
This entity is chimeric
Mutation(s): 0 
Gene Names: AF_2299RSal33209_2010
EC: 2.7.8
Membrane Entity: Yes 
UniProt
Find proteins for A9WSF5 (Renibacterium salmoninarum (strain ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235))
Explore A9WSF5 
Go to UniProtKB:  A9WSF5
Find proteins for O27985 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O27985 
Go to UniProtKB:  O27985
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA9WSF5O27985
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8K6
Query on 8K6

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
D [auth A]
E [auth A]
Octadecane
C18 H38
RZJRJXONCZWCBN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
DA [auth A],
EA [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.204 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.632α = 90
b = 94.069β = 90
c = 103.916γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 8K6Click on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description