1GYM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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 pho ...

    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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C
A
298Bacillus cereusMutation(s): 0 
EC: 4.6.1.13
Find proteins for P14262 (Bacillus cereus)
Go to UniProtKB:  P14262
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYG
Query on MYG

Download SDF File 
Download CCD File 
A
GLUCOSAMINYL-(ALPHA-6)-D-MYO-INOSITOL
C12 H23 N O10
HEPUIGACZYVUCD-YZRQSVRMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MYGIC50: 2000000 nM BINDINGMOAD
MYGIC50: 2000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.200α = 90.00
b = 46.500β = 90.00
c = 161.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
DETECTORdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance