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: 2.30 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 

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

  • DOI: 10.1016/s0003-9861(03)00343-6
  • Primary Citation of Related Structures:  
    1P5X, 1P6E, 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-type enzyme, we tentatively identified Asp55 as the general base for the enzymatic reaction ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase CA245Bacillus cereusMutation(s): 1 
Gene Names: plc
EC: 3.1.4.3
UniProt
Find proteins for P09598 (Bacillus cereus)
Explore P09598 
Go to UniProtKB:  P09598
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PC5
Query on PC5

Download Ideal Coordinates CCD File 
E [auth A]1,2-DI-N-PENTANOYL-SN-GLYCERO-3-DITHIOPHOSPHOCHOLINE
C18 H36 N O6 P S2
WEXRBKRFCBLWEL-MRXNPFEDSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PC5Ki :  1210000   nM  PDBBind
PC5Ki:  1210000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.167 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.795α = 90
b = 89.795β = 90
c = 74.206γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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