1UNE

CARBOXYLIC ESTER HYDROLASE, 1.5 ANGSTROM ORTHORHOMBIC FORM OF THE BOVINE RECOMBINANT PLA2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

High-resolution refinement of orthorhombic bovine pancreatic phospholipase A2.

Sekar, K.Sundaralingam, M.

(1999) Acta Crystallogr D Biol Crystallogr 55: 46-50

  • DOI: 10.1107/S0907444998006568
  • Primary Citation of Related Structures:  
    1UNE

  • PubMed Abstract: 
  • The X-ray structure of recombinant bovine pancreatic phospholipase A2 (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 A resolution. The crystal belongs to the space group P212121 with unit-cell parameters a = 47 ...

    The X-ray structure of recombinant bovine pancreatic phospholipase A2 (PLA2), which specifically catalyzes the cleavage of the sn-2 acylester bond of phospholipids, has been refined at 1.5 A resolution. The crystal belongs to the space group P212121 with unit-cell parameters a = 47.12, b = 64.59 and c = 38.14 A similar to the native enzyme reported previously by Dijkstra et al. [J. Mol. Biol. (1981), 147, 97-123]. The refinement converged to an R value of 18.4% (Rfree = 22.8%) for 16 374 reflections between 10.0 and 1.5 A resolution. The surface-loop residues (60-70) are ordered in the present orthorhombic recombinant enzyme, but disordered in the trigonal recombinant enzyme. The active-site residues, His48, Asp99, and the catalytic water superimpose well with the trigonal form. Besides the catalytic water which is hydrogen bonded to His48, it is often seen that there is a second water attached to the same N atom of His48 and simultaneously hydrogen bonded to the O atom of Asp49. It is thought that the second water facilitates the tautomerism of His48 for enzyme catalysis. The catalytic water is also hydrogen bonded to the equatorial water coordinated to the calcium ion. In addition to the equatorial water, there is also an axial calcium water and the additional structural water. These five common water molecules are hydrogen bonded to the additional 16 water molecules in the present orthorhombic structure which may further enhance the structural integrity of the active site. Besides the protein and one calcium ion, a total of 134 water molecules were located in the present high-resolution refinement.


    Related Citations: 
    • Crystal Structure of the Complex of Bovine Pancreatic Phospholipase A2 with a Transition State Analogue
      Sekar, K., Kumar, A., Liu, X., Tsai, M.-D., Gelb, M.H., Sundaralingam, M.
      () To be published --: --
    • 1.72A Resolution Refinement of the Trigonal Form of Bovine Pancreatic Phospholipase A2
      Sekar, K., Sekarudu, C., Tsai, M.-D., Sundaralingam, M.
      () To be published --: --
    • Crystal Structure of the Complex of Bovine Pancreatic Phospholipase A2 with the Inhibitor 1-Hexadecyl-3-(Trifluoroethyl)-Sn-Glycero-2-Phosphomethanol
      Sekar, K., Eswaramoorthy, S., Jain, M.K., Sundaralingam, M.
      (1997) Biochemistry 36: 14186
    • 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
    • Phospholipase A2 Engineering. Deletion of the C-Terminus Segment Changes Substrate Specificity and Uncouples Calcium and Substrate Binding at the Zwitterionic Interface
      Huang, B., Yu, B.Z., Rogers, J., Byeon, I.J., Sekar, K., Chen, X., Sundaralingam, M., Tsai, M.D., Jain, M.K.
      (1996) Biochemistry 35: 12164
    • Phospholipase A2 Engineering. X-Ray Structural and Functional Evidence for the Interaction of Lysine-56 with Substrates
      Noel, J.P., Bingman, C.A., Deng, T.L., Dupureur, C.M., Hamilton, K.J., Jiang, R.T., Kwak, J.G., Sekharudu, C., Sundaralingam, M., Tsai, M.D.
      (1991) Biochemistry 30: 11801

    Organizational Affiliation

    Biological Macromolecular Structure Center, Departments of Chemistry and Biochemistry, 100 W 18th Avenue, The Ohio State University, Columbus, OH 43210, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2A123Bos taurusMutation(s): 0 
Gene Names: MATURE PLA2PLA2G1B
EC: 3.1.1.4
UniProt
Find proteins for P00593 (Bos taurus)
Explore P00593 
Go to UniProtKB:  P00593
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.12α = 90
b = 64.59β = 90
c = 38.14γ = 90
Software Package:
Software NamePurpose
R-AXISdata collection
R-AXISdata reduction
X-PLORmodel building
X-PLORrefinement
R-AXISdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1997-11-05 
  • Released Date: 1998-05-06 
  • Deposition Author(s): Sundaralingam, M.

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-04
    Changes: Data collection, Other
  • Version 1.4: 2018-04-11
    Changes: Data collection