2BD1

A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 

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This is version 1.3 of the entry. See complete history


Literature

Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A(2).

Sekar, K.Yogavel, M.Kanaujia, S.P.Sharma, A.Velmurugan, D.Poi, M.J.Dauter, Z.Tsai, M.D.

(2006) Acta Crystallogr D Biol Crystallogr 62: 717-724

  • DOI: 10.1107/S0907444906014855
  • Primary Citation of Related Structures:  
    2BCH, 2BD1

  • PubMed Abstract: 
  • The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A2 (PLA2) have been solved and refined at 1.9 and 1.1 A resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion ...

    The crystal structures of the monoclinic and trigonal forms of the quadruple mutant K53,56,120,121M of recombinant bovine pancreatic phospholipase A2 (PLA2) have been solved and refined at 1.9 and 1.1 A resolution, respectively. Interestingly, the monoclinic form reveals the presence of the second calcium ion. Furthermore, the surface-loop residues are ordered and the conformation of residues 62-66 is similar to that observed in other structures containing the second calcium ion. On the other hand, in the trigonal form the surface loop is disordered and the second calcium is absent. Docking studies suggest that the second calcium and residues Lys62 and Asp66 from the surface loop could be involved in the interaction with the polar head group of the membrane phospholipid. It is hypothesized that the two structures of the quadruple mutant, monoclinic and trigonal, represent the conformations of PLA2 at the lipid interface and in solution, respectively. A docked structure with a phospholipid molecule and with a transition-state analogue bound, one at the active site coordinating to the catalytic calcium and the other at the second calcium site, but both at the i-face, is presented.


    Organizational Affiliation

    Bioinformatics Centre, Indian Institute of Science, Bangalore 560 012, India. sekar@physics.iisc.ernet.in



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipase A2A, B123Bos taurusMutation(s): 4 
Gene Names: PLA2G1B
EC: 3.1.1.4
UniProt
Find proteins for P00593 (Bos taurus)
Explore P00593 
Go to UniProtKB:  P00593
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.58α = 90
b = 48.69β = 102.3
c = 67.55γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection, Refinement description