1HN4

PROPHOSPHOLIPASE A2 DIMER COMPLEXED WITH MJ33, SULFATE, AND CALCIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The basis for k(cat) impairment in prophospholipase A(2) from the anion-assisted dimer structure.

Epstein, T.M.Yu, B.Z.Pan, Y.H.Tutton, S.P.Maliwal, B.P.Jain, M.K.Bahnson, B.J.

(2001) Biochemistry 40: 11411-11422


  • PubMed Abstract: 
  • Kinetic results in this paper show that, contrary to earlier reports, pig pancreatic prophospholipase A(2) (proPLA2) does not hydrolyze monodisperse short chain phosphatidylcholine below the critical micelle concentration. ProPLA2 is active on an ani ...

    Kinetic results in this paper show that, contrary to earlier reports, pig pancreatic prophospholipase A(2) (proPLA2) does not hydrolyze monodisperse short chain phosphatidylcholine below the critical micelle concentration. ProPLA2 is active on an anionic interface, but at a rate that is decreased by more than 100-fold compared to that of PLA2, the active form. Solution studies show that both proPLA2 and PLA2 bind to an anionic interface and also bind a tetrahedral intermediate mimic at the active site. The 1.5 A resolution crystal structure of the anion-assisted dimer of proPLA2 reported in this paper is compared with the corresponding structure for PLA2 [Pan, Y. H., et al. (2001) Biochemistry 40, 609-617]. As a mimic for the forms bound to the anionic interface, these structures provide insights into the possible structural basis for the impaired chemical step of the zymogen. The proPLA2 dimer contained within one crystallographic asymmetric unit has one molecule of the inhibitor 1-hexadecyl-3-(trifluoroethyl)-sn-glycero-2-phosphomethanol and is bridged by four coplanar sulfate anions. Relative to the structure of PLA2, the subunit contact surface in proPLA2 displays a tilted orientation, an altered mode of inhibitor binding, displacement of a mechanistically significant loop that includes Tyr69, and a critical active site water seen in PLA2 that is not seen in proPLA2. These differences are interpreted to suggest possible origins of the functional differences between the pro and active enzyme at an anionic interface. A structural origin of this difference is discussed in terms of the calcium-coordinated activated water mechanism of the esterolysis reaction. Together, a comparison of the structures of the anion-assisted dimers of PLA2 and proPLA2 not only offers an explanation of why the zymogen form is k(cat)-impaired and binds poorly even to the anionic interface but also supports a mechanism for the activated enzyme that includes a critical second-sphere assisting water bridging His48 and the calcium-coordinated catalytic water.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Delaware, Newark 19716, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROPHOSPHOLIPASE A2
A, B
131Sus scrofaGene Names: PLA2G1B
EC: 3.1.1.4
Find proteins for P00592 (Sus scrofa)
Go to Gene View: PLA2G1B
Go to UniProtKB:  P00592
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MJI
Query on MJI

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Download CCD File 
A
1-HEXADECYL-3-TRIFLUOROETHYL-SN-GLYCERO-2-PHOSPHATE METHANE
MJ33 INHIBITOR
C22 H44 F3 O6 P
XPTFBVFCGHXMRK-OAQYLSRUSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MJIKd: 150000 nM BINDINGMOAD
MJIKd: 150000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.215 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.488α = 90.00
b = 54.852β = 104.06
c = 56.896γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-12-05
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance