1KPM

First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 

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This is version 1.4 of the entry. See complete history


Literature

First Structural Evidence of a Specific Inhibition of Phospholipase A2 by alpha-Tocopherol (Vitamin E) and its Implications in Inflammation: Crystal Structure of the Complex Formed Between Phospholipase A2 and alpha-Tocopherol at 1.8 A Resolution

Chandra, V.Jasti, J.Kaur, P.Betzel, C.Srinivasan, A.Singh, T.P.

(2002) J Mol Biol 320: 215-222

  • DOI: 10.1016/S0022-2836(02)00473-4
  • Primary Citation of Related Structures:  
    1KPM

  • PubMed Abstract: 
  • This is the first structural evidence of alpha-tocopherol (alpha-TP) as a possible candidate against inflammation, as it inhibits phospholipase A2 specifically and effectively. The crystal structure of the complex formed between Vipera russelli phospholipase A2 and alpha-tocopherol has been determined and refined to a resolution of 1 ...

    This is the first structural evidence of alpha-tocopherol (alpha-TP) as a possible candidate against inflammation, as it inhibits phospholipase A2 specifically and effectively. The crystal structure of the complex formed between Vipera russelli phospholipase A2 and alpha-tocopherol has been determined and refined to a resolution of 1.8 A. The structure contains two molecules, A and B, of phospholipase A2 in the asymmetric unit, together with one alpha-tocopherol molecule, which is bound specifically to one of them. The phospholipase A2 molecules interact extensively with each other in the crystalline state. The two molecules were found in a stable association in the solution state as well, thus indicating their inherent tendency to remain together as a structural unit, leading to significant functional implications. In the crystal structure, the most important difference between the conformations of two molecules as a result of their association pertains to the orientation of Trp31. It may be noted that Trp31 is located at the mouth of the hydrophobic channel that forms the binding domain of the enzyme. The values of torsion angles (phi, psi, chi(1) and chi(2)) for both the backbone as well as for the side-chain of Trp31 in molecules A and B are -94 degrees, -30 degrees, -66 degrees, 116 degrees and -128 degrees, 170 degrees, -63 degrees, -81 degrees, respectively. The conformation of Trp31 in molecule A is suitable for binding, while that in B hinders the passage of the ligand to the binding site. Consequently, alpha-tocopherol is able to bind to molecule A only, while the binding site of molecule B contains three water molecules. In the complex, the aromatic moiety of alpha-tocopherol is placed in the large space at the active site of the enzyme, while the long hydrophobic channel in the enzyme is filled by hydrocarbon chain of alpha-tocopherol. The critical interactions between the enzyme and alpha-tocopherol are generated between the hydroxyl group of the six-membered ring of alpha-tocopherol and His48 N(delta1) and Asp49 O(delta1) as characteristic hydrogen bonds. The remaining part of alpha-tocopherol interacts extensively with the residues of the hydrophobic channel of the enzyme, giving rise to a number of hydrophobic interactions, resulting in the formation of a stable complex.


    Related Citations: 
    • First Structural Evidence of Antiinflammatory Action of Vitamin E (2,5,7,8-tetramethyl-2-(4',8',12'-trimethyltridecyl)-6-chromanol) Through its Binding to Phospholipase A2 Specifically: Crystal Structure of a Complex Formed between Phospholipase A2 and Vitamin E at 1.80 Resolution
      Chandra, V., Jasti, J., Kaur, P., Betzel, C., Srinivasan, A., Singh, T.P.
      () To be published --: --
    • Crystal Structure of a Complex Formed between Phospholipase A2 from Daboia russelli pulchella and a Designed Pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 Resolution
      Chandra, V., Jasti, J., Kaur, P., Betzel, C., Srinivasan, A., Singh, T.P.
      () To be published --: --
    • First Structural Evidence of the Inhibition of Phospholipase A2 by Aristolochic Acid: Crystal Structure of a Complex Formed between Phospholipase A2 and Aristolochic Acid
      Chandra, V., Jasti, J., Kaur, P., Betzel, C., Srinivasan, A., Singh, T.P.
      () To be published --: --
    • Design of Specific Inhibitors of Phospholipase A2: Crystal Structure of a Complex Formed between Phospholipase A2 from Daboia russelli pulchella and a Designed Pentapeptide Leu-Ala-Ile-Tyr-Ser at 2.0 Resolution
      Chandra, V., Jasti, J., Kaur, P., Betzel, C., Srinivasan, A., Singh, T.P.
      () To be published --: --
    • Regulation of catalytic function by molecular association: structure of phospholipase A2 from Daboia russelli pulchella (DPLA2) at 1.9 A resolution.
      Chandra, V., Kaur, P., Jasti, J., Betzel, C., Singh, T.P.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 1793
    • Three-dimensional structure of a presynaptic neurotoxic phospholipase A2 from Daboia russelli pulchella at 2.4 A resolution.
      Chandra, V., Kaur, P., Srinivasan, A., Singh, T.P.
      (2000) J Mol Biol 296: 1117

    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase A2A, B121Daboia russelii pulchellaMutation(s): 0 
EC: 3.1.1.4
UniProt
Find proteins for P59071 (Daboia russelii)
Explore P59071 
Go to UniProtKB:  P59071
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59071
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
VIT Binding MOAD:  1KPM Ki: 1590 (nM) from 1 assay(s)
PDBBind:  1KPM Ki: 1590 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.197 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.79α = 90
b = 88.51β = 90
c = 78.04γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2017-10-11
    Changes: Refinement description