1GYM

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

Summary for 1GYM

• Entry DOI: 10.2210/pdb1gym/pdb
• Descriptor: PHOSPHATIDYLINOSITOL-SPECIFIC PHOSPHOLIPASE C, (1R,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside (3 entities in total)
• Functional Keywords: phosphatidylinositol specific phospholipase c, glucosaminyl (alpha-1-6)-d-myo-inositol, inhibitor complex, hydrolase (phosphoric diester), lipid degradation
• Biological source: Bacillus cereus
• Cellular location: Secreted: P14262
• Total number of polymer chains: 1
• Total formula weight: 34909.98

Authors

Heinz, D.W.,Ryan, M.,Smith, M.P.,Weaver, L.H.,Keana, J.F.W.,Griffith, O.H. (deposition date: 1996-05-02, release date: 1996-11-08, Last modification date: 2024-02-07)

Primary citation

Heinz, D.W.,Ryan, M.,Smith, M.P.,Weaver, L.H.,Keana, J.F.,Griffith, O.H.
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.
Biochemistry, 35:9496-9504, 1996

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. 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.

PubMed: 8755729
DOI: 10.1021/bi9606105

Experimental method

X-RAY DIFFRACTION (2.2 Å)