1DJX

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-1,4,5-TRISPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.220 

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This is version 1.2 of the entry. See complete history


Literature

Structural mapping of the catalytic mechanism for a mammalian phosphoinositide-specific phospholipase C.

Essen, L.O.Perisic, O.Katan, M.Wu, Y.Roberts, M.F.Williams, R.L.

(1997) Biochemistry 36: 1704-1718

  • DOI: 10.1021/bi962512p
  • Primary Citation of Related Structures:  
    1DJW, 1DJX, 1DJY, 1DJZ

  • PubMed Abstract: 
  • The crystal structures of various ternary complexes of phosphoinositide-specific phospholipase C-delta 1 from rat with calcium and inositol phosphates have been determined at 2.30-2.95 A resolution. The inositol phosphates used in this study mimic the binding of substrates and the reaction intermediate and include D-myo-inositol-1,4,5-trisphosphate, D-myo-inositol-2,4, 5-trisphosphate ...

    The crystal structures of various ternary complexes of phosphoinositide-specific phospholipase C-delta 1 from rat with calcium and inositol phosphates have been determined at 2.30-2.95 A resolution. The inositol phosphates used in this study mimic the binding of substrates and the reaction intermediate and include D-myo-inositol-1,4,5-trisphosphate, D-myo-inositol-2,4, 5-trisphosphate. D-myo-inositol-4,5-bisphosphate, and D,1-myo-inositol-2-methylene-1,2-cyclićmonophosphonate. The complexes exhibit an almost invariant mode of binding in the active site, each fitting edge-on into the active site and interacting with both the enzyme and the catalytic calcium at the bottom of the active site. Most of the active site residues do not undergo conformational changes upon binding either calcium or inositol phosphates. The structures are consistent with bidentate liganding of the catalytic calcium to the inositol phosphate intermediate and transition state. The complexes suggest explanations for substrate preference, pH optima, and ratio of cyclic to acyclic reaction products. A reaction mechanism is derived that supports general acid/base catalysis in a sequential mechanism involving a cyclic phosphate intermediate and rules out a parallel mechanism where acyclic and cyclic products are simultaneously generated.


    Related Citations: 
    • Crystal Structure of a Mammalian Phosphoinositide-Specific Phospholipase C Delta
      Essen, L.O., Perisic, O., Cheung, R., Katan, M., Williams, R.L.
      (1996) Nature 380: 595

    Organizational Affiliation

    Centre for Protein Engineering, MRC Centre, Cambridge, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1A, B624Rattus norvegicusMutation(s): 0 
Gene Names: CDNA FRAGMENTPlcd1
EC: 3.1.4.11
UniProt
Find proteins for P10688 (Rattus norvegicus)
Explore P10688 
Go to UniProtKB:  P10688
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
I3P Binding MOAD:  1DJX Kd: 1700 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.220 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 397.54α = 90
b = 397.54β = 90
c = 397.54γ = 90
Software Package:
Software NamePurpose
TNTrefinement
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance