4IJO

Unraveling hidden allosteric regulatory sites in structurally homologues metalloproteases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.188 

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
  • Primary Citation of Related Structures:  
    4IJO

  • 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 antagonists targeting enzyme catalytic moieties specific to one of the homologous enzymes often appears to be an extremely difficult task ...

    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 U S A 102(15): 5334

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Macrophage metalloelastase A158Homo sapiensMutation(s): 1 
Gene Names: MMP12HME
EC: 3.4.24.65
Find proteins for P39900 (Homo sapiens)
Explore P39900 
Go to UniProtKB:  P39900
NIH Common Fund Data Resources
PHAROS:  P39900
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.435α = 90
b = 60.164β = 114.8
c = 53.777γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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