4IJO

Unraveling hidden allosteric regulatory sites in structurally homologues metalloproteases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Unraveling hidden regulatory sites in structurally homologous metalloproteases

Udi, Y.Fragai, M.Grossman, M.Mitternacht, S.Arad-Yellin, R.Calderone, V.Melikian, M.Toccafondi, M.Berezovsky, I.N.Luchinat, C.Sagi, I.

(2013) J.Mol.Biol. 425: 2330-2346

  • DOI: 10.1016/j.jmb.2013.04.009

  • PubMed Abstract: 
  • Monitoring enzymatic activity in vivo of individual homologous enzymes such as the matrix metalloproteinases (MMPs) by antagonist molecules is highly desired for defining physiological and pathophysiological pathways. However, the rational design of ...

    Monitoring enzymatic activity in vivo of individual homologous enzymes such as the matrix metalloproteinases (MMPs) by antagonist molecules is highly desired for defining physiological and pathophysiological pathways. However, the rational design of antagonists targeting enzyme catalytic moieties specific to one of the homologous enzymes often appears to be an extremely difficult task. This is mainly due to the high structural homology at the enzyme active sites shared by members of the protein family. Accordingly, controlling enzymatic activity via alternative allosteric sites has become an attractive proposition for drug design targeting individual homologous enzymes. Yet, the challenge remains to identify such regulatory alternative sites that are often hidden and scattered over different locations on the protein's surface. We have designed branched amphiphilic molecules exhibiting specific inhibitory activity towards individual members of the MMP family. These amphiphilic isomers share the same chemical nature, providing versatile nonspecific binding reactivity that allows to probe hidden regulatory residues on a given protein surface. Using the advantage provided by amphiphilic ligands, here we explore a new approach for determining hidden regulatory sites. This approach includes diverse experimental analysis, such as structural spectroscopic analyses, NMR, and protein crystallography combined with computational prediction of effector binding sites. We demonstrate how our approach works by analyzing members of the MMP family that possess a unique set of such sites. Our work provides a proof of principle for using ligand effectors to unravel hidden regulatory sites specific to members of the structurally homologous MMP family. This approach may be exploited for the design of novel molecular effectors and therapeutic agents affecting protein catalytic function via interactions with structure-specific regulatory sites.


    Related Citations: 
    • Snapshots of the reaction mechanism of matrix metalloproteinases
      Bertini, I.,Calderone, V.,Fragai, M.,Luchinat, C.,Maletta, M.,Yeo, K.J.
      (2006) Angew. Chem. Int. Ed. Engl. 45(47): 7952
    • Conformational variability of matrix metalloproteinases: beyond a single 3D structure
      Bertini, I.,Calderone, V.,Cosenza, M.,Fragai, M.,Lee, Y.M.,Luchinat, C.,Mangani, S.,Terni, B.,Turano, P.
      (2005) Proc.Natl.Acad.Sci.USA 102(15): 5334


    Organizational Affiliation

    Department of Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage metalloelastase
A
158Homo sapiensMutation(s): 1 
Gene Names: MMP12 (HME)
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Go to Gene View: MMP12
Go to UniProtKB:  P39900
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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: 0.232 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 50.435α = 90.00
b = 60.164β = 114.80
c = 53.777γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
CrysalisProdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-01
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description