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Hydrolase PDB id
3ptd
Jmol
Contents
Protein chain
296 a.a. *
Waters ×122
* Residue conservation analysis
PDB id:
3ptd
Name: Hydrolase
Title: Phosphatidylinositol-specific phospholipasE C mutant d274s
Structure: Phosphatidylinositol-specific phospholipasE C. Chain: a. Synonym: pi-plc. Engineered: yes. Mutation: yes
Source: Bacillus cereus. Organism_taxid: 1396. Cellular_location: secreted into medium. Gene: pi-plc gene. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: gene cloned in escherichia coli
Resolution:
2.20Å     R-factor:   0.177     R-free:   0.262
Authors: D.W.Heinz
Key ref:
C.S.Gässler et al. (1997). Probing the roles of active site residues in phosphatidylinositol-specific phospholipase C from Bacillus cereus by site-directed mutagenesis. Biochemistry, 36, 12802-12813. PubMed id: 9335537 DOI: 10.1021/bi971102d
Date:
17-Jul-97     Release date:   21-Jan-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P14262  (PLC_BACCE) -  1-phosphatidylinositol phosphodiesterase
Seq:
Struc: 		329 a.a.
296 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.4.6.1.13  - Phosphatidylinositol diacylglycerol-lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      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
 + 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   1 term 
  Biological process     lipid metabolic process   2 terms 
  Biochemical function     lyase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi971102d Biochemistry 36:12802-12813 (1997)
PubMed id: 9335537  
 
 
Probing the roles of active site residues in phosphatidylinositol-specific phospholipase C from Bacillus cereus by site-directed mutagenesis.
C.S.Gässler, M.Ryan, T.Liu, O.H.Griffith, D.W.Heinz.
 
  ABSTRACT  
 
The role of amino acid residues located in the active site pocket of phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus cereus[Heinz, D. W., Ryan, M., Bullock, T., & Griffith, O. H. (1995) EMBO J. 14, 3855-3863] was investigated by site-directed mutagenesis, kinetics, and crystal structure analysis. Twelve residues involved in catalysis and substrate binding (His32, Arg69, His82, Gly83, Lys115, Glu117, Arg163, Trp178, Asp180, Asp198, Tyr200, and Asp274) were individually replaced by 1-3 other amino acids, resulting in a total number of 21 mutants. Replacements in the mutants H32A, H32L, R69A, R69E, R69K, H82A, H82L, E117K, R163I, D198A, D198E, D198S, Y200S, and D274S caused essentially complete inactivation of the enzyme. The remaining mutants (G83S, K115E, R163K, W178Y, D180S, Y200F, and D274N) exhibited reduced activities up to 57% when compared with wild-type PI-PLC. Crystal structures determined at a resolution ranging from 2.0 to 2.7 A for six mutants (H32A, H32L, R163K, D198E, D274N, and D274S) showed that significant changes were confined to the site of the respective mutation without perturbation of the rest of the structure. Only in mutant D198E do the side chains of two neighboring arginine residues move across the inositol binding pocket toward the newly introduced glutamic acid. An analysis of these structure-function relationships provides new insight into the catalytic mechanism, and suggests a molecular explanation of some of the substrate stereospecificity and inhibitor binding data available for this enzyme.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19548649 M.Pu, M.F.Roberts, and A.Gershenson (2009).
Fluorescence correlation spectroscopy of phosphatidylinositol-specific phospholipase C monitors the interplay of substrate and activator lipid binding.
  Biochemistry, 48, 6835-6845.  
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.  
16493657 B.Nocek, M.Cuff, E.Evdokimova, A.Edwards, A.Joachimiak, and A.Savchenko (2006).
1.6 A crystal structure of a PA2721 protein from pseudomonas aeruginosa--a potential drug-resistance protein.
  Proteins, 63, 1102-1105.
PDB code: 1u69
15155721 L.Zhao, H.Liao, and M.D.Tsai (2004).
The catalytic role of aspartate in a short strong hydrogen bond of the Asp274-His32 catalytic dyad in phosphatidylinositol-specific phospholipase C can be substituted by a chloride ion.
  J Biol Chem, 279, 31995-32000.  
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.  
  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.  
9636030 L.W.Schultz, D.J.Quirk, and R.T.Raines (1998).
His...Asp catalytic dyad of ribonuclease A: structure and function of the wild-type, D121N, and D121A enzymes.
  Biochemistry, 37, 8886-8898.
PDB codes: 3rsd 4rsd
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.