1DJY

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-2,4,5-TRISPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 

wwPDB Validation 3D Report Full Report


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, 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 th ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1
A, B
624Rattus norvegicusGene Names: Plcd1
EC: 3.1.4.11
Find proteins for P10688 (Rattus norvegicus)
Go to UniProtKB:  P10688
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
I2P
Query on I2P

Download SDF File 
Download CCD File 
A, B
D-MYO-INOSITOL-2,4,5-TRIPHOSPHATE
D-MYO-INOSITOL-2,4,5-TRISPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-LKPKBOIGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.210 
  • Space Group: F 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 397.130α = 90.00
b = 397.130β = 90.00
c = 397.130γ = 90.00
Software Package:
Software NamePurpose
CCP4model building
TNTrefinement
CCP4phasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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