PDBsum entry 2plc

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protein links
Hydrolase PDB id
Protein chain
274 a.a. *
Waters ×102
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Phosphatidylinositol-specific phospholipasE C from listeria monocytogenes
Structure: Phosphatidylinositol-specific phospholipasE C. Chain: a. Synonym: pi-plc. Engineered: yes
Source: Listeria monocytogenes. Organism_taxid: 1639. Strain: egd serotype 1-2a. Cell_line: bl21. Cellular_location: secreted into medium. Gene: plca. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
2.00Å     R-factor:   0.198     R-free:   0.249
Authors: D.W.Heinz,J.Moser
Key ref:
J.Moser et al. (1997). Crystal structure of the phosphatidylinositol-specific phospholipase C from the human pathogen Listeria monocytogenes. J Mol Biol, 273, 269-282. PubMed id: 9367761 DOI: 10.1006/jmbi.1997.1290
09-Jul-97     Release date:   14-Jan-98    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P34024  (PLC_LISMO) -  1-phosphatidylinositol phosphodiesterase
317 a.a.
274 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Phosphatidylinositol diacylglycerol-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

1-Phosphatidyl-myo-inositol Metabolism
      Reaction: 1-phosphatidyl-1D-myo-inositol = 1D-myo-inositol 1,2-cyclic phosphate + 1,2-diacyl-sn-glycerol
= 1D-myo-inositol 1,2-cyclic phosphate
+ 1,2-diacyl-sn-glycerol
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     lipid metabolic process   3 terms 
  Biochemical function     lyase activity     3 terms  


DOI no: 10.1006/jmbi.1997.1290 J Mol Biol 273:269-282 (1997)
PubMed id: 9367761  
Crystal structure of the phosphatidylinositol-specific phospholipase C from the human pathogen Listeria monocytogenes.
J.Moser, B.Gerstel, J.E.Meyer, T.Chakraborty, J.Wehland, D.W.Heinz.
The X-ray crystal structure of the phosphatidylinositol-specific phospholipase C (PI-PLC) from the human pathogen Listeria monocytogenes has been determined both in free form at 2.0 A resolution, and in complex with the competitive inhibitor myo-inositol at 2.6 A resolution. The structure was solved by a combination of molecular replacement using the structure of Bacillus cereus PI-PLC and single isomorphous replacement. The enzyme consists of a single (beta alpha)8-barrel domain with the active site located at the C-terminal side of the beta-barrel. Unlike other (beta alpha)8-barrels, the barrel in PI-PLC is open because it lacks hydrogen bonding interactions between beta-strands V and VI. myo-Inositol binds to the active site pocket by making specific hydrogen bonding interactions with a number of charged amino acid side-chains as well as a coplanar stacking interaction with a tyrosine residue. Despite a relatively low sequence identity of approximately 24%, the structure is highly homologous to that of B.cereus PI-PLC with an r.m.s. deviation for 228 common C alpha positions of 1.46 A. Larger differences are found for loop regions that accommodate most of the numerous amino acid insertions and deletions. The active site pocket is also well conserved with only two amino acid replacements directly implicated in inositol binding.
  Selected figure(s)  
Figure 1.
Figure 1. Reaction catalyzed by L.monocytogenes PI-PLC.
Figure 10.
Figure 10. Side-by-side view of the molecular surfaces of BPI-PLC (left) and LPI-PLC (right) showing the C-terminal side of the b-barrel with the active site pocket in the center, where negative potentials on the surface are shaded in red and positive potentials in blue. myo-Inositol bound to the active site pocket is depicted by yellow bonds. The hydrophobic ridge is designated by A, the extended GPI-binding site by B. The picture was generated using the pro- gram GRASP (Nicholls, 1993).
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 273, 269-282) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19472261 T.Böttcher, and S.A.Sieber (2009).
Beta-lactones decrease the intracellular virulence of Listeria monocytogenes in macrophages.
  ChemMedChem, 4, 1260-1263.  
19281241 W.Chen, H.Goldfine, B.Ananthanarayanan, W.Cho, and M.F.Roberts (2009).
Listeria monocytogenes phosphatidylinositol-specific phospholipase C: Kinetic activation and homing in on different interfaces.
  Biochemistry, 48, 3578-3592.  
18214971 A.S.Ozyurt, and T.L.Selby (2008).
Computational active site analysis of molecular pathways to improve functional classification of enzymes.
  Proteins, 72, 184-196.  
18310040 S.Témoin, S.M.Roche, O.Grépinet, Y.Fardini, and P.Velge (2008).
Multiple point mutations in virulence genes explain the low virulence of Listeria monocytogenes field strains.
  Microbiology, 154, 939-948.  
17213187 C.Shao, X.Shi, H.Wehbi, C.Zambonelli, J.F.Head, B.A.Seaton, and M.F.Roberts (2007).
Dimer structure of an interfacially impaired phosphatidylinositol-specific phospholipase C.
  J Biol Chem, 282, 9228-9235.
PDB code: 2or2
16118276 Z.Wei, L.A.Zenewicz, and H.Goldfine (2005).
Listeria monocytogenes phosphatidylinositol-specific phospholipase C has evolved for virulence by greatly reduced activity on GPI anchors.
  Proc Natl Acad Sci U S A, 102, 12927-12931.  
16177340 Z.Wei, P.Schnupf, M.A.Poussin, L.A.Zenewicz, H.Shen, and H.Goldfine (2005).
Characterization of Listeria monocytogenes expressing anthrolysin O and phosphatidylinositol-specific phospholipase C from Bacillus anthracis.
  Infect Immun, 73, 6639-6646.  
12714598 J.Feng, W.D.Bradley, and M.F.Roberts (2003).
Optimizing the interfacial binding and activity of a bacterial phosphatidylinositol-specific phospholipase C.
  J Biol Chem, 278, 24651-24657.  
12440695 F.J.Sharom, and M.T.Lehto (2002).
Glycosylphosphatidylinositol-anchored proteins: structure, function, and cleavage by phosphatidylinositol-specific phospholipase C.
  Biochem Cell Biol, 80, 535-549.  
11912206 J.Feng, H.Wehbi, and M.F.Roberts (2002).
Role of tryptophan residues in interfacial binding of phosphatidylinositol-specific phospholipase C.
  J Biol Chem, 277, 19867-19875.  
11331006 R.J.Kubiak, X.Yue, R.J.Hondal, C.Mihai, M.D.Tsai, and K.S.Bruzik (2001).
Involvement of the Arg-Asp-His catalytic triad in enzymatic cleavage of the phosphodiester bond.
  Biochemistry, 40, 5422-5432.  
10992479 H.Goldfine, S.J.Wadsworth, and N.C.Johnston (2000).
Activation of host phospholipases C and D in macrophages after infection with Listeria monocytogenes.
  Infect Immun, 68, 5735-5741.  
  9864213 T.Bannam, and H.Goldfine (1999).
Mutagenesis of active-site histidines of Listeria monocytogenes phosphatidylinositol-specific phospholipase C: effects on enzyme activity and biological function.
  Infect Immun, 67, 182-186.  
9838022 M.Katan (1998).
Families of phosphoinositide-specific phospholipase C: structure and function.
  Biochim Biophys Acta, 1436, 5.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.