4JQG

Crystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate with a fluorine atom.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Halogen Bonding Controls Selectivity of FRET Substrate Probes for MMP-9.

Tranchant, I., Vera, L., Czarny, B., Amoura, M., Cassar, E., Beau, F., Stura, E.A., Dive, V.

(2014) Chem Biol 21: 408-413

  • DOI: 10.1016/j.chembiol.2014.01.008
  • Primary Citation of Related Structures:  
    4JIJ, 4JQG

  • PubMed Abstract: 

    • Matrix metalloproteinases (MMPs) are a large family of zinc-dependent endoproteases that catalyze cleavage of extracellular matrix and nonmatrix proteins. MMPs play a role in tissue remodeling, and their uncontrolled activity is associated with number of diseases, including tumor metastasis ...

    Matrix metalloproteinases (MMPs) are a large family of zinc-dependent endoproteases that catalyze cleavage of extracellular matrix and nonmatrix proteins. MMPs play a role in tissue remodeling, and their uncontrolled activity is associated with number of diseases, including tumor metastasis. Thus, there is a need to develop methods to monitor MMP activity, and number of probes has been previously described. The key problem many probes encounter is the issue of selectivity, since 23 human MMPs, despite playing different physiological roles, have structurally similar active sites. Here, we introduce the halogen bonding concept into the probe design and show that the probe containing iodine exhibits an unprecedented selectivity for MMP-9. We provide structure-based explanation for the selectivity, confirming that it is due to formation of the halogen bond that supports catalysis, and we highlight the value of exploring halogen bonding in the context of selective probe design.

    Organizational Affiliation: 

    CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France. Electronic address: vincent.dive@cea.fr.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2) P, Q9N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Matrix metalloproteinase-9 A, B164Homo sapiensMutation(s): 1 
Gene Names: CLG4B, MMP9
EC: 3.4.24.35
Find proteins for P14780 (Homo sapiens)
Explore P14780 
Go to UniProtKB:  P14780
NIH Common Fund Data Resources
PHAROS:  P14780
GTEx:  ENSG00000100985
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
SR
Query on SR
Download Ideal Coordinates CCD File 
A, B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N		 Ligand Interaction
PGO
Query on PGO
Download Ideal Coordinates CCD File 
A, B
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
AZI
Query on AZI
Download Ideal Coordinates CCD File 
P, Q
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DNW
Query on DNW		P,QL-PEPTIDE LINKINGC9 H10 N4 O6ALA
PFF
Query on PFF		P,QL-PEPTIDE LINKINGC9 H10 F N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.14α = 90
b = 57.48β = 90
c = 171.42γ = 90
Software Package:
Software NamePurpose
DNAdata collection
MOLREPphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-12
    Type: Initial release
  • Version 1.1: 2014-04-16
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Data collection, Refinement description, Source and taxonomy