5FYO

Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, crystal form 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The structure of a calcium-dependent phosphoinositide-specific phospholipase C from Pseudomonas sp. 62186, the first from a Gram-negative bacterium.

Moroz, O.V.Blagova, E.Lebedev, A.A.Nrgaard, A.Segura, D.R.Blicher, T.H.Brask, J.Wilson, K.S.

(2017) Acta Crystallogr D Struct Biol 73: 32-44

  • DOI: https://doi.org/10.1107/S2059798316019616
  • Primary Citation of Related Structures:  
    5FYO, 5FYP, 5FYR

  • PubMed Abstract: 

    Bacterial phosphoinositide-specific phospholipases C (PI-PLCs) are the smallest members of the PI-PLC family, which includes much larger mammalian enzymes responsible for signal transduction as well as enzymes from protozoan parasites, yeast and plants. Eukaryotic PI-PLCs have calcium in the active site, but this is absent in the known structures of Gram-positive bacteria, where its role is instead played by arginine. In addition to their use in a number of industrial applications, the bacterial enzymes attract special interest because they can serve as convenient models of the catalytic domains of eukaryotic enzymes for in vitro activity studies. Here, the structure of a PI-PLC from Pseudomonas sp. 62186 is reported, the first from a Gram-negative bacterium and the first of a native bacterial PI-PLC with calcium present in the active site. Solution of the structure posed particular problems owing to the low sequence identity of available homologous structures. Its dependence on calcium for catalysis makes this enzyme a better model for studies of the mammalian PI-PLCs than the previously used calcium-independent bacterial PI-PLCs.


  • Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
A, B
298Pseudomonas sp.Mutation(s): 0 
UniProt
Find proteins for A0A1S4NYD4 (Pseudomonas sp)
Explore A0A1S4NYD4 
Go to UniProtKB:  A0A1S4NYD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1S4NYD4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.127 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.08α = 90
b = 96.08β = 90
c = 113.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Advisory, Data collection
  • Version 2.0: 2019-05-08
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation
  • Version 2.1: 2024-01-10
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description