1POA

INTERFACIAL CATALYSIS: THE MECHANISM OF PHOSPHOLIPASE A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Interfacial catalysis: the mechanism of phospholipase A2.

Scott, D.L.White, S.P.Otwinowski, Z.Yuan, W.Gelb, M.H.Sigler, P.B.

(1990) Science 250: 1541-1546

  • DOI: 10.1126/science.2274785
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A chemical description of the action of phospholipase A2 (PLA2) can now be inferred with confidence from three high-resolution x-ray crystal structures. The first is the structure of the PLA2 from the venom of the Chinese cobra (Naja naja atra) in a ...

    A chemical description of the action of phospholipase A2 (PLA2) can now be inferred with confidence from three high-resolution x-ray crystal structures. The first is the structure of the PLA2 from the venom of the Chinese cobra (Naja naja atra) in a complex with a phosphonate transition-state analogue. This enzyme is typical of a large, well-studied homologous family of PLA2S. The second is a similar complex with the evolutionarily distant bee-venom PLA2. The third structure is the uninhibited PLA2 from Chinese cobra venom. Despite the different molecular architectures of the cobra and bee-venom PLA2s, the transition-state analogue interacts in a nearly identical way with the catalytic machinery of both enzymes. The disposition of the fatty-acid side chains suggests a common access route of the substrate from its position in the lipid aggregate to its productive interaction with the active site. Comparison of the cobra-venom complex with the uninhibited enzyme indicates that optimal binding and catalysis at the lipid-water interface is due to facilitated substrate diffusion from the interfacial binding surface to the catalytic site rather than an allosteric change in the enzyme's structure. However, a second bound calcium ion changes its position upon the binding of the transition-state analogue, suggesting a mechanism for augmenting the critical electrophile.


    Related Citations: 
    • Crystal Structure of Cobra-Venom Phospholipase A2 in a Complex with a Transition-State Analogue
      White, S.P., Scott, D.L., Otwinowski, Z., Gelb, M.H., Sigler, P.B.
      (1990) Science 250: 1560

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
118Naja atraMutation(s): 0 
EC: 3.1.1.4
Find proteins for P00598 (Naja atra)
Go to UniProtKB:  P00598
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93α = 90
b = 93β = 90
c = 22.2γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROFFTrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-17
    Changes: Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description