1KVW

CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT H48Q OF BOVINE PANCREATIC PLA2 ENZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A2.

Sekar, K.Biswas, R.Li, Y.Tsai, M.Sundaralingam, M.

(1999) Acta Crystallogr D Biol Crystallogr 55: 443-447

  • DOI: 10.1107/s0907444998013699
  • Primary Citation of Related Structures:  
    1KVY, 1KVX, 1KVW

  • PubMed Abstract: 
  • Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 A resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121 ...

    Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A2 have been determined at around 1.9 A resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P212121. The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3121. The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.


    Related Citations: 
    • The High Resolution Refinement of the Orthorhombic Bovine Pancreatic Phospholipase A2
      Sekar, K., Sundaralingam, M.
      () To be published --: --
    • 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., Sundaralingam, M.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 342
    • 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, Department of Chemistry, Ohio State Biochemistry Program, 012 Rightmire Hall, 1060 Carmack Road, The Ohio State University, Columbus, OH 43210, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHOLIPASE A2 A123Bos taurusMutation(s): 1 
Gene Names: MATURE PLA2PLA2G1B
EC: 3.1.1.4
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 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.12α = 90
b = 47.12β = 90
c = 102.88γ = 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: 1998-04-24 
  • Released Date: 1998-11-18 
  • Deposition Author(s): Sundaralingam, M.

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-18
    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