1P6E

STRUCTURE OF THE D55N MUTANT OF PHOSPHOLIPASE C FROM BACILLUS CEREUS IN COMPLEX WITH 1,2-DI-N-PENTANOYL-SN-GLYCERO-3-DITHIOPHOSPHOCHOLINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Using X-ray crystallography of the Asp55Asn mutant of the phosphatidylcholine-preferring phospholipase C from Bacillus cereus to support the mechanistic role of Asp55 as the general base.

Antikainen, N.M.Monzingo, A.F.Franklin, C.L.Robertus, J.D.Martin, S.F.

(2003) Arch.Biochem.Biophys. 417: 81-86

  • Primary Citation of Related Structures:  1P5X, 1P6D

  • PubMed Abstract: 
  • Because mutations of the ionizable Asp at position 55 of the phosphatidylcholine preferring phospholipase C from Bacillus cereus (PLC(Bc)) to a non-ionizable Asn generate a mutant enzyme (D55N) with 10(4)-fold lower catalytic activity than the wild-t ...

    Because mutations of the ionizable Asp at position 55 of the phosphatidylcholine preferring phospholipase C from Bacillus cereus (PLC(Bc)) to a non-ionizable Asn generate a mutant enzyme (D55N) with 10(4)-fold lower catalytic activity than the wild-type enzyme, we tentatively identified Asp55 as the general base for the enzymatic reaction. To eliminate the alternate possibility that Asp55 is a structurally important amino acid, the X-ray structures of unbound D55N and complexes of D55N with two non-hydrolyzable substrate analogues have been solved and refined to 2.0, 2.0, and 2.3A, respectively. The structures of unbound wild-type PLC(Bc) and a wild-type PLC(Bc)-complex with a non-hydrolyzable substrate analogue do not change significantly as a result of replacing Asp55 with Asn. These observations demonstrate that Asp55 is not critical for the structural integrity of the enzyme and support the hypothesis that Asp55 is the general base in the PLC(Bc)-catalyzed hydrolysis of phospholipids.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phospholipase C
A
245Bacillus cereusGene Names: plc
EC: 3.1.4.3
Find proteins for P09598 (Bacillus cereus)
Go to UniProtKB:  P09598
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PC5
Query on PC5

Download SDF File 
Download CCD File 
A
1,2-DI-N-PENTANOYL-SN-GLYCERO-3-DITHIOPHOSPHOCHOLINE
C18 H36 N O6 P S2
WEXRBKRFCBLWEL-MRXNPFEDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PC5Ki: 1210000 nM BINDINGMOAD
PC5Ki: 1210000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.163 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 89.795α = 90.00
b = 89.795β = 90.00
c = 74.206γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-30
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance