PDBsum entry: 1gym

Hydrolase (phosphoric diester)

PDB id: 1gym

Contents

Protein chain

296 a.a. *

Ligands

MYG

Waters ×127

* Residue conservation analysis

PDB id:

1gym

Name:

Hydrolase (phosphoric diester)

Title:

Phosphatidylinositol-specific phospholipasE C in complex with glucosamine-(alpha-1-6)-myo-inositol

Structure:

Phosphatidylinositol-specific phospholipasE C. Chain: a. Engineered: yes

Source:

Bacillus cereus. Organism_taxid: 1396. Gene: pi-plc gene. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.178 R-free: 0.272

Authors:

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

Key ref:

D.W.Heinz et al. (1996). 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. PubMed id: 8755729 DOI: 10.1021/bi9606105

Date:

02-May-96 Release date: 08-Nov-96

Protein chain

P14262  (PLC_BACCE) -  1-phosphatidylinositol phosphodiesterase

Seq: 329 a.a.

Struc: 296 a.a.

Enzyme reactions

• Enzyme class: E.C.4.6.1.13 - Phosphatidylinositol diacylglycerol-lyase.
• Pathway: 1-Phosphatidyl-myo-inositol Metabolism
• Reaction: 1-phosphatidyl-1D-myo-inositol = 1D-myo-inositol 1,2-cyclic phosphate + 1,2-diacyl-sn-glycerol

1-phosphatidyl-1D-myo-inositol = 1D-myo-inositol 1,2-cyclic phosphate (Bound ligand (Het Group name = MYG) matches with 46.00% similarity) + 1,2-diacyl-sn-glycerol

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biological process: lipid metabolic process (2 terms)
• Biochemical function: lyase activity (4 terms)

reference

DOI no: 10.1021/bi9606105

Biochemistry 35:9496-9504 (1996)

PubMed id: 8755729

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.

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

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.