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: 1.849 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 

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:  

  • 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 numbe ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)
P, Q
9N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Matrix metalloproteinase-9
A, B
164Homo sapiensMutation(s): 1 
Gene Names: MMP9 (CLG4B)
EC: 3.4.24.35
Find proteins for P14780 (Homo sapiens)
Go to Gene View: MMP9
Go to UniProtKB:  P14780
Small Molecules
Ligands 8 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
AZI
Query on AZI

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P, Q
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

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A, B
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
SR
Query on SR

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A, B
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
P, Q
NON-POLYMERH2 N

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PFF
Query on PFF
P, Q
L-PEPTIDE LINKINGC9 H10 F N O2PHE
8MC
Query on 8MC
P, Q
NON-POLYMERC12 H10 O5

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DNW
Query on DNW
P, Q
L-PEPTIDE LINKINGC9 H10 N4 O6ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.849 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.140α = 90.00
b = 57.480β = 90.00
c = 171.420γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
MOLREPphasing
DNAdata collection
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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