2B96

Third Calcium ion found in an inhibitor bound phospholipase A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.202 

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This is version 1.2 of the entry. See complete history


Literature

Third Calcium ion found in an inhibitor bound phospholipase A2

Sekar, K.Gayathri, D.Velmurugan, D.Jeyakanthan, J.Yamane, T.Poi, M.J.Tsai, M.D.

(2006) Acta Crystallogr D Biol Crystallogr 62: 392-397

  • DOI: 10.1107/S0907444906001612
  • Primary Citation of Related Structures:  
    2B96

  • PubMed Abstract: 
  • The lipolytic enzyme phospholipase A2 plays a crucial role in lipid metabolism and catalyzes hydrolysis of the fatty-acid ester bond at the sn-2 position of phospholipids. Here, the crystal structure (1.7 A resolution) of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 complexed with an organic molecule, p-methoxybenzoic acid (anisic acid), is reported ...

    The lipolytic enzyme phospholipase A2 plays a crucial role in lipid metabolism and catalyzes hydrolysis of the fatty-acid ester bond at the sn-2 position of phospholipids. Here, the crystal structure (1.7 A resolution) of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 complexed with an organic molecule, p-methoxybenzoic acid (anisic acid), is reported. Residues 60-70 (the surface-loop residues) are ordered and adopt conformations which are different from those normally found in structures in which a second calcium ion is present. It is interesting to note that for the first time a third calcium ion has been identified. In addition, four Tris (2-amino-2-hydroxymethyl-1,3-propanediol) molecules were located. It is believed that one of the Tris molecules plays a role in clamping the third calcium ion and that another is involved in controlling the dynamics of the surface loop through hydrogen bonds.


    Related Citations: 
    • Atomic resolution (0.97 A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2
      Sekar, K., Rajakannan, V., Gayathri, D., Velmurugan, D., Poi, M.J., Dauter, M., Dauter, Z., Tsai, M.D.
      (2005) Acta Crystallogr Sect F Struct Biol Cryst Commun 61: 3
    • Crystal structures of the free and anisic acid bound triple mutant of phospholipase A2.
      Sekar, K., Mala, S.V., Yogavel, M., Velmurugan, D., Poi, M.J., Vishwanath, B.S., Gowda, T.V., Jeyaprakash, A.A., Tsai, M.D.
      (2003) J Mol Biol 333: 367
    • Observation of additional calcium ion in the crystal structure of the triple mutant K56,120,121M of bovine pancreatic phospholipase A2.
      Rajakannan, V., Yogavel, M., Poi, M.J., Jeyaprakash, A.A., Jeyakanthan, J., Velmurugan, D., Tsai, M.D., Sekar, K.
      (2002) J Mol Biol 324: 755
    • High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2.
      Sekar, K., Sundaralingam, M.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 46
    • Phospholipase A2 engineering. Structural and functional roles of the highly conserved active site residue aspartate-99.
      Sekar, K., Yu, B.Z., Rogers, J., Lutton, J., Liu, X., Chen, X., Tsai, M.D., Jain, M.K., Sundaralingam, M.
      (1997) Biochemistry 36: 3104

    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 A2A123Bos taurusMutation(s): 3 
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: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.202 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.19α = 90
b = 46.19β = 90
c = 102.86γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance