1GYM

PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C IN COMPLEX WITH GLUCOSAMINE-(ALPHA-1-6)-MYO-INOSITOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with glucosaminyl(alpha 1-->6)-D-myo-inositol, an essential fragment of GPI anchors.

Heinz, D.W.Ryan, M.Smith, M.P.Weaver, L.H.Keana, J.F.Griffith, O.H.

(1996) Biochemistry 35: 9496-9504

  • DOI: 10.1021/bi9606105
  • Primary Citation of Related Structures:  
    1GYM

  • PubMed Abstract: 
  • Numerous proteins on the external surface of the plasma membrane are anchored by glycosylated derivatives of phosphatidylinositol (GPI), rather than by hydrophobic amino acids embedded in the phospholipid bilayer. These GPI anchors are cleaved by phosphatidylinositol-specific phospholipases C (PI-PLCs) to release a water-soluble protein with an exposed glycosylinositol moiety and diacylglycerol, which remains in the membrane ...

    Numerous proteins on the external surface of the plasma membrane are anchored by glycosylated derivatives of phosphatidylinositol (GPI), rather than by hydrophobic amino acids embedded in the phospholipid bilayer. These GPI anchors are cleaved by phosphatidylinositol-specific phospholipases C (PI-PLCs) to release a water-soluble protein with an exposed glycosylinositol moiety and diacylglycerol, which remains in the membrane. We have previously determined the crystal structure of Bacillus cereus PI-PLC, the enzyme which is widely used to release GPI-anchored proteins from membranes, as free enzyme and also in complex with myo-inositol [Heinz, D.W., Ryan, M. Bullock, T.L., & Griffith, O. H. (1995) EMBO J. 14, 3855-3863]. Here we report the refined 2.2 A crystal structure of this enzyme complexed with a segment of the core of all GPI anchors, glucosaminyl(alpha 1-->6)-D-myo-inositol [GlcN-(alpha 1-->6)Ins ]. The myo-inositol moiety of GlcN(alpha 1-->6)Ins is well-defined and occupies essentially the same position in the active site as does free myo-inositol, which provides convincing evidence that the enzyme utilizes the same catalytic mechanism for cleavage of PI and GPI anchors. The myo-inositol moiety makes several specific hydrogen bonding interactions with active site residues. In contrast, the glucosamine moiety lies exposed to solvent at the entrance of the active site with minimal specific protein contacts. The glucosamine moiety is also less well-defined, suggesting enhanced conformational flexibility. On the basis of the positioning of GlcN(alpha 1-->6)Ins in the active site, it is predicted that the remainder of the GPI-glycan makes little or no specific interactions with B. cereus PI-PLC. This explains why B. cereus PI-PLC can cleave GPI anchors having variable glycan structures.


    Related Citations: 
    • Crystal Structure of the Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus in Complex with Myo-Inositol
      Heinz, D.W., Ryan, M., Bullock, T.L., Griffith, O.H.
      (1995) EMBO J 14: 3855
    • Crystallization of Phosphatidylinositol-Specific Phospholipase C from Bacillus Cereus
      Bullock, T.L., Ryan, M., Kim, S.L., Remington, S.J., Griffith, O.H.
      (1993) Biophys J 64: 784
    • Phosphatidylinositol-Specific Phospholipase C of Bacillus Cereus: Cloning, Sequencing, and Relationship to Other Phospholipases
      Kuppe, A., Evans, L.M., Mcmillen, D.A., Griffith, O.H.
      (1989) J Bacteriol 171: 6077

    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Universität Freiburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE CA298Bacillus cereusMutation(s): 0 
Gene Names: PI-PLC GENE
EC: 3.1.4.10 (PDB Primary Data), 4.6.1.13 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P14262 (Bacillus cereus)
Explore P14262 
Go to UniProtKB:  P14262
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14262
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYG
Query on MYG

Download Ideal Coordinates CCD File 
B [auth A](1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
C12 H23 N O10
HEPUIGACZYVUCD-YZRQSVRMSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MYG Binding MOAD:  1GYM IC50: 2.00e+6 (nM) from 1 assay(s)
PDBBind:  1GYM IC50: 2.00e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.2α = 90
b = 46.5β = 90
c = 161γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DETECTORdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary