1KVX

CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT D99A OF BOVINE PANCREATIC PLA2, 1.9 A ORTHORHOMBIC FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.200 

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.,Sect.D 55: 443-447

  • Primary Citation of Related Structures:  

  • 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 grou ...

    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: 
    • 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. 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
    • 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.,Sect.D 54: 334
    • The High Resolution Refinement of the Orthorhombic Bovine Pancreatic Phospholipase A2
      Sekar, K.,Sundaralingam, M.
      () TO BE PUBLISHED --: --
    • 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
    • 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.,Sect.D 54: 342


    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
123Bos taurusMutation(s): 1 
Gene Names: PLA2G1B
EC: 3.1.1.4
Find proteins for P00593 (Bos taurus)
Go to Gene View: PLA2G1B
Go to UniProtKB:  P00593
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.313 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.560α = 90.00
b = 64.570β = 90.00
c = 37.990γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
R-AXISdata reduction
R-AXISdata collection
X-PLORmodel building
R-AXISdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-04-28 
  • Released Date: 1998-11-18 
  • Deposition Author(s): Sundaralingam, M.

Revision History 

  • Version 1.0: 1998-11-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-04-04
    Type: Data collection, Other
  • Version 1.4: 2018-04-11
    Type: Data collection