3UTZ

Endogenous-like inhibitory antibodies targeting activated metalloproteinase motifs show therapeutic potential


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Antibodies targeting the catalytic zinc complex of activated matrix metalloproteinases show therapeutic potential.

Sela-Passwell, N.Kikkeri, R.Dym, O.Rozenberg, H.Margalit, R.Arad-Yellin, R.Eisenstein, M.Brenner, O.Shoham, T.Danon, T.Shanzer, A.Sagi, I.

(2012) NAT.MED. (N.Y.) 18: 143-147

  • DOI: 10.1038/nm.2582

  • PubMed Abstract: 
  • Endogenous tissue inhibitors of metalloproteinases (TIMPs) have key roles in regulating physiological and pathological cellular processes. Imitating the inhibitory molecular mechanisms of TIMPs while increasing selectivity has been a challenging but ...

    Endogenous tissue inhibitors of metalloproteinases (TIMPs) have key roles in regulating physiological and pathological cellular processes. Imitating the inhibitory molecular mechanisms of TIMPs while increasing selectivity has been a challenging but desired approach for antibody-based therapy. TIMPs use hybrid protein-protein interactions to form an energetic bond with the catalytic metal ion, as well as with enzyme surface residues. We used an innovative immunization strategy that exploits aspects of molecular mimicry to produce inhibitory antibodies that show TIMP-like binding mechanisms toward the activated forms of gelatinases (matrix metalloproteinases 2 and 9). Specifically, we immunized mice with a synthetic molecule that mimics the conserved structure of the metalloenzyme catalytic zinc-histidine complex residing within the enzyme active site. This immunization procedure yielded selective function-blocking monoclonal antibodies directed against the catalytic zinc-protein complex and enzyme surface conformational epitopes of endogenous gelatinases. The therapeutic potential of these antibodies has been demonstrated with relevant mouse models of inflammatory bowel disease. Here we propose a general experimental strategy for generating inhibitory antibodies that effectively target the in vivo activity of dysregulated metalloproteinases by mimicking the mechanism employed by TIMPs.


    Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metalloproteinase, light chain
A, D, E
219N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Metalloproteinase, heavy chain
B, C, F
225N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C, D, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.095α = 90.00
b = 108.369β = 111.91
c = 86.466γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
HKL-2000data reduction
DNAdata collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2012-03-21
    Type: Database references
  • Version 1.2: 2013-10-02
    Type: Source and taxonomy
  • Version 1.3: 2014-03-26
    Type: Database references
  • Version 1.4: 2017-03-15
    Type: Structure summary