5FYR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1107/S2059798316019616
  • Primary Citation of Related Structures:  

  • 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 plan ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOINOSITOL-SPECIFIC PHOSPHOLIPASE C
A, B, C, D
298N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
INS
Query on INS

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Download CCD File 
A, B, C, D
1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
MYO-INOSITOL
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.145 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 135.443α = 90.00
b = 135.443β = 90.00
c = 113.732γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation