1MKV

CARBOXYLIC ESTER HYDROLASE COMPLEX (PLA2 + TRANSITION STATE ANALOG COMPLEX)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 334-341


  • PubMed Abstract: 
  • The 1.89 A resolution structure of the complex of bovine pancreatic phospholipase A2 (PLA2) with the transition-state analogue L-1-O-octyl-2-heptylphosphonyl-sn-glycero-3-phosphoethanolamine (TSA) has been determined. The crystal of the complex is tr ...

    The 1.89 A resolution structure of the complex of bovine pancreatic phospholipase A2 (PLA2) with the transition-state analogue L-1-O-octyl-2-heptylphosphonyl-sn-glycero-3-phosphoethanolamine (TSA) has been determined. The crystal of the complex is trigonal, space group P3121, a = b = 46.58 and c = 102.91 A and isomorphous to the native recombinant wild type (WT). The structure was refined to a final crystallographic R value of 18.0% including 957 protein atoms, 88 water molecules, one calcium ion and all 31 non-H atoms of the inhibitor at 1.89 A resolution. In all, 7 726 reflections [F>2sigma(F)] were used between 8.0 and 1.89 A resolution. The inhibitor is deeply locked into the active-site cleft and coordinates to the calcium ion by displacing the two water molecules in the calcium pentagonal bipyramid by the anionic O atoms of the phosphate and phosphonate group. The hydroxyl group of Tyr69 hydrogen bonds to the second anionic O atom of the phosphate group while that of the phosphonate group replaces the third water, 'catalytic' water, which forms a hydrogen bond to Ndelta1 of His48. The fourth water which also shares Ndelta1 of His48 is displaced by the steric hinderance of the inhibitor. The fifth conserved structural water is still present in the active site and forms a network of hydrogen bonds with the surrounding residues. The structure is compared to the other known TSA-PLA2 complexes.


    Related Citations: 
    • 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 Angstrom Resolution Refinement of the Trigonal Form of Bovine Pancreatic Phospholipase A2
      Sekar, K.,Sekharudu, C.,Tsai, M.-D.,Sundaralingam, M.
      () TO BE PUBLISHED --: --
    • 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
    • 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


    Organizational Affiliation

    Biological Macromolecular Structure Center, Departments of Chemistry and Biochemistry, 100 West 18th Avenue, The Ohio State University, Columbus, OH 43210-1185, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2
A
123Bos taurusMutation(s): 0 
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 2 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
GEL
Query on GEL

Download SDF File 
Download CCD File 
A
1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
C20 H45 N O8 P2
RCCNUBYROFOKAU-HXUWFJFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Work: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 46.580α = 90.00
b = 46.580β = 90.00
c = 102.910γ = 120.00
Software Package:
Software NamePurpose
XENGENdata reduction
XENGENdata scaling
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
XENGENdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-09-13 
  • Released Date: 1998-03-18 
  • Deposition Author(s): Sundaralingam, M.

Revision History 

  • Version 1.0: 1998-03-18
    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: 2018-03-07
    Type: Data collection, Other