2WQ5

Non-antibiotic properties of tetracyclines: structural basis for inhibition of secretory phospholipase A2.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Non-Antibiotic Properties of Tetracyclines: Structural Basis for Inhibition of Secretory Phospholipase A(2).

Dalm, D.Palm, G.J.Aleksandrov, A.Simonson, T.Hinrichs, W.

(2010) J.Mol.Biol. 398: 83

  • DOI: 10.1016/j.jmb.2010.02.049

  • PubMed Abstract: 
  • Secretory phospholipase A(2) is involved in inflammatory processes and was previously shown to be inhibited by lipophilic tetracyclines such as minocycline (minoTc) and doxycycline. Lipophilic tetracyclines might be a new lead compound for the design ...

    Secretory phospholipase A(2) is involved in inflammatory processes and was previously shown to be inhibited by lipophilic tetracyclines such as minocycline (minoTc) and doxycycline. Lipophilic tetracyclines might be a new lead compound for the design of specific inhibitors of secretory phospholipase A(2), which play a crucial role in inflammatory processes. Our X-ray crystal structure analysis at 1.65 A resolution of the minoTc complex of phospholipase A(2) (PLA(2)) of the Indian cobra (Naja naja naja) is the first example of nonantibiotic tetracycline interactions with a protein. MinoTc interferes with the conformation of the active-site Ca(2+)-binding loop, preventing Ca(2)(+) binding, and shields the active site from substrate entrance, resulting in inhibition of the enzyme. MinoTc binding to PLA(2) is dominated by hydrophobic interactions quite different from antibiotic recognition of tetracyclines by proteins or the ribosome. The affinity of minoTc for PLA(2) was determined by surface plasmon resonance, resulting in a dissociation constant K(d)=1.8 x 10(-)(4) M.


    Organizational Affiliation

    Institute for Biochemistry, Department of Molecular Structural Biology, University of Greifswald, Felix-Hausdorff-Str. 4, D-17489 Greifswald, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOLIPASE A2, ACIDIC
A
119Naja najaMutation(s): 0 
EC: 3.1.1.4
Find proteins for P15445 (Naja naja)
Go to UniProtKB:  P15445
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MIY
Query on MIY

Download SDF File 
Download CCD File 
A
(4S,4AS,5AR,12AS)-4,7-BIS(DIMETHYLAMINO)-3,10,12,12A-TETRAHYDROXY-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
MINOCYCLINE
C23 H27 N3 O7
DYKFCLLONBREIL-KVUCHLLUSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MIYKd: 180000 nM BINDINGMOAD
MIYKd: 180000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 68.712α = 90.00
b = 68.712β = 90.00
c = 68.712γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-06-28
    Type: Data collection