1FDK

CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.280 
  • 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

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: 14186-14191

  • DOI: 10.1021/bi971370b
  • Primary Citation of Related Structures:  
    1FDK

  • PubMed Abstract: 
  • The structure of recombinant bovine pancreatic phospholipase A2 (PLA2) complexed with the competitive inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero -2-phosphomethanol (hereafter MJ33), a phospholipid analogue without the sn-3 phosphodiester group, has been determined ...

    The structure of recombinant bovine pancreatic phospholipase A2 (PLA2) complexed with the competitive inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero -2-phosphomethanol (hereafter MJ33), a phospholipid analogue without the sn-3 phosphodiester group, has been determined. The crystals are trigonal, space group P3121, a = b = 46.36 A and c = 102.56 A, and isomorphous to the recombinant PLA2 with one molecule in the asymmetric unit. The structure was refined using 8082 reflections between 8.0 and 1.91 A resolution to a final R-value of 18.4% [Rfree = 28.0%]. The model includes 957 protein atoms, 86 water molecules, one calcium ion, and 26 non-hydrogen atoms of the inhibitor MJ33. The overall tertiary fold of the complex is very similar to that of the inhibitor-free recombinant PLA2 with a root mean square deviation of 0.32 A for all the backbone atoms. The electron density of the surface loop residues 62-66 is clear and ordered, unlike the other trigonal bovine PLA2 structures done to date. This structural change could be responsible for the interfacial allosteric activation, which thermodynamically relates the enhanced binding of the substrate mimic to the active site of the enzyme. MJ33 is tightly bound in the active-site cleft, dislodging the equatorial coordinated calcium water (W5), the putative catalytic water W6, and the neighboring water W7. The axial coordinated calcium water is missing; thus the hexacoordinated calcium is a monocapped pentagonal pyramid. Although MJ33 is a sn-2 tetrahedral mimic, its phosphate binds to PLA2 differently from the sn-2 phosphonate analogue of phospholipids, another tetrahedral mimic. The knowledge of the active-site geometry of MJ33 would be useful in the design of more useful therapeutic agents for PLA2.


    Related Citations: 
    • 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.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 334
    • 1.72 A Resolution Refinement of the Trigonal Form of Bovine Pancreatic Phospholipase A2
      Sekar, K., Sekharudu, C., Tsai, M.-D., Sundaralingam, M.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 342
    • 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, Department of Chemistry, Ohio State University, Columbus, Ohio 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLE
Query on GLE

Download Ideal Coordinates CCD File 
C [auth A]1-DECYL-3-TRIFLUORO ETHYL-SN-GLYCERO-2-PHOSPHOMETHANOL
C16 H32 F3 O6 P
YBCDZAGHRGXDRX-HNNXBMFYSA-N
 Ligand Interaction
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: 1.91 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.36α = 90
b = 46.36β = 90
c = 102.56γ = 120
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: 1997-09-04 
  • Released Date: 1998-10-14 
  • Deposition Author(s): Sundaralingam, M.

Revision History  (Full details and data files)

  • Version 1.0: 1998-10-14
    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