4JQG | pdb_00004jqg

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

• PDB DOI: https://doi.org/10.2210/pdb4JQG/pdb

• Classification: HYDROLASE/substrate
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-03-20 Released: 2014-03-12 
• Deposition Author(s): Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Tranchant, I., Amoura, M., Dive, V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.242 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.193 (Depositor) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

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

• PubMed: 24583051 
• DOI: https://doi.org/10.1016/j.chembiol.2014.01.008
• Primary Citation 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. 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.

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Organizational Affiliation: 
• CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France.
CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 40.33 kDa 
• Atom Count: 3,322 
• Modeled Residue Count: 346 
• Deposited Residue Count: 346 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)	A [auth P], C [auth Q]	9	N/A	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Matrix metalloproteinase-9	B [auth A], D [auth B]	164	Homo sapiens	Mutation(s): 1  Gene Names: CLG4B, MMP9 EC: 3.4.24.35
UniProt & NIH Common Fund Data Resources
Find proteins for P14780 (Homo sapiens) Explore P14780  Go to UniProtKB:  P14780
PHAROS:  P14780 GTEx:  ENSG00000100985

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SR	I [auth A], V [auth B], W [auth B]	STRONTIUM ION Sr PWYYWQHXAPXYMF-UHFFFAOYSA-N
PGO	Q [auth A], X [auth B]	S-1,2-PROPANEDIOL C3 H8 O2 DNIAPMSPPWPWGF-VKHMYHEASA-N
ZN	F [auth A], G [auth A], S [auth B], T [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	K [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
AZI	E [auth P], R [auth Q]	AZIDE ION N3 IVRMZWNICZWHMI-UHFFFAOYSA-N
CA	H [auth A], J [auth A], U [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	AA [auth B], BA [auth B], CA [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DNW	A [auth P], C [auth Q]	L-PEPTIDE LINKING	C9 H10 N4 O6		ALA
PFF	A [auth P], C [auth Q]	L-PEPTIDE LINKING	C9 H10 F N O2		PHE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.242 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.193 (Depositor) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.14	α = 90
b = 57.48	β = 90
c = 171.42	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Stura, E.A., Vera, L., Cassar-Lajeunesse, E., Tranchant, I., Amoura, M., Dive, V.

Revision History  

• 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
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection