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- PDB-4jqg: Crystal structure of an inactive mutant of MMP-9 catalytic domain... -

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Basic information

Entry
Database: PDB / ID: 4jqg
TitleCrystal structure of an inactive mutant of MMP-9 catalytic domain in complex with a fluorogenic synthetic peptidic substrate with a fluorine atom.
Components
  • Matrix metalloproteinase-9
  • fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)
KeywordsHYDROLASE/substrate / halogen-water-hydrogen bridge / Zincin-like / Gelatinase / Collagenase / Catalytic Domain / HYDROLASE-substrate complex
Function / homology
Function and homology information


gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / endodermal cell differentiation ...gelatinase B / negative regulation of epithelial cell differentiation involved in kidney development / negative regulation of cation channel activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular response to UV-A / positive regulation of keratinocyte migration / regulation of neuroinflammatory response / positive regulation of epidermal growth factor receptor signaling pathway / Assembly of collagen fibrils and other multimeric structures / endodermal cell differentiation / Activation of Matrix Metalloproteinases / positive regulation of release of cytochrome c from mitochondria / response to amyloid-beta / macrophage differentiation / Collagen degradation / collagen catabolic process / EPH-ephrin mediated repulsion of cells / extracellular matrix disassembly / ephrin receptor signaling pathway / positive regulation of DNA binding / negative regulation of intrinsic apoptotic signaling pathway / positive regulation of vascular associated smooth muscle cell proliferation / cellular response to cadmium ion / collagen binding / embryo implantation / Degradation of the extracellular matrix / extracellular matrix organization / positive regulation of receptor binding / skeletal system development / Signaling by SCF-KIT / metalloendopeptidase activity / cellular response to reactive oxygen species / metallopeptidase activity / cell migration / tertiary granule lumen / peptidase activity / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / endopeptidase activity / cellular response to lipopolysaccharide / ficolin-1-rich granule lumen / Extra-nuclear estrogen signaling / positive regulation of protein phosphorylation / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / Neutrophil degranulation / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular exosome / zinc ion binding / extracellular region / identical protein binding
Similarity search - Function
Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site ...Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Kringle-like fold / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / S-1,2-PROPANEDIOL / STRONTIUM ION / Matrix metalloproteinase-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
AuthorsStura, E.A. / Vera, L. / Cassar-Lajeunesse, E. / Tranchant, I. / Amoura, M. / Dive, V.
CitationJournal: Chem.Biol. / Year: 2014
Title: Halogen Bonding Controls Selectivity of FRET Substrate Probes for MMP-9.
Authors: Tranchant, I. / Vera, L. / Czarny, B. / Amoura, M. / Cassar, E. / Beau, F. / Stura, E.A. / Dive, V.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
P: fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)
A: Matrix metalloproteinase-9
Q: fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,32729
Polymers38,8514
Non-polymers1,47625
Water7,710428
1
P: fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)
A: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,24515
Polymers19,4252
Non-polymers81913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-92 kcal/mol
Surface area8460 Å2
MethodPISA
2
Q: fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)
B: Matrix metalloproteinase-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,08314
Polymers19,4252
Non-polymers65712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-140 kcal/mol
Surface area8680 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-250 kcal/mol
Surface area15770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.140, 57.480, 171.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide / Protein , 2 types, 4 molecules PQAB

#1: Protein/peptide fluorogenic peptidic substrate (8MC)PLG(PFF)(DNW)AR(NH2)


Mass: 1145.157 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: fluorogenic synthetic L-peptide substrate with lower catalytic efficiency with MMP-9 than the iodine containing substrate PDB code 4JIJ.
#2: Protein Matrix metalloproteinase-9 / / MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB / 67 kDa matrix ...MMP-9 / 92 kDa gelatinase / 92 kDa type IV collagenase / Gelatinase B / GELB / 67 kDa matrix metalloproteinase-9 / 82 kDa matrix metalloproteinase-9


Mass: 18280.283 Da / Num. of mol.: 2 / Mutation: E402A
Source method: isolated from a genetically manipulated source
Details: Catalytic domain construct: 110-216 and 392-444 Mutagenesis: Glu402Ala Structur e: renumbered omitting missing domain.
Source: (gene. exp.) Homo sapiens (human) / Gene: CLG4B, MMP9 / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3 star) / References: UniProt: P14780, gelatinase B

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Non-polymers , 9 types, 453 molecules

#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SR / STRONTIUM ION / Strontium


Mass: 87.620 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Sr
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL / Propanediol


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#10: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Protein: hMMP9 E402A at 420 microM + AHA 120mM 0.12 M acetohydroxamic acid and 0.5 microL IT34-F at 10 milli-M. Reservoir: 10% PEG 20K, 0.1 M MMT (L-malic acid, MES, Tris) 75% acid/25% ...Details: Protein: hMMP9 E402A at 420 microM + AHA 120mM 0.12 M acetohydroxamic acid and 0.5 microL IT34-F at 10 milli-M. Reservoir: 10% PEG 20K, 0.1 M MMT (L-malic acid, MES, Tris) 75% acid/25% basic, 0.5 M NaCl, 0.02 SrCl2, 10% glycerol. Cryoprotectant: 10% Di-ethylene glycol, 5% glycerol, 10% propanediol, 5% dioxane, .8 M Li formate, 9% PEG 10,000 0.1M (MMT 75/25), pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972981 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2013 / Details: mirrors
RadiationMonochromator: Channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972981 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. all: 29876 / Num. obs: 29657 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.46 % / Biso Wilson estimate: 25.048 Å2 / Rmerge(I) obs: 0.343 / Rsym value: 0.325 / Net I/σ(I): 5.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.85-1.968.351.0452.2347210.97998.4
1.96-2.18.250.7863.0744730.73699.1
2.1-2.268.520.633.8641630.5999.3
2.26-2.488.090.5194.6138650.48599.2
2.48-2.778.780.4075.8234790.38399.5
2.77-3.28.450.2797.1231350.26399.4
3.2-3.919.120.1719.1826590.16299.8
3.91-5.518.640.1859.7421130.17100
5.51-508.130.1279.4512680.11999.8

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JIJ

4jij


Resolution: 1.849→40.524 Å / SU ML: 0.22 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / σ(I): -3 / Phase error: 26.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1481 4.99 %to match 4JIJ reference
Rwork0.1931 ---
all0.1946 29657 --
obs0.1956 29655 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.048 Å2
Refinement stepCycle: LAST / Resolution: 1.849→40.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2764 0 63 428 3255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072978
X-RAY DIFFRACTIONf_angle_d1.1154053
X-RAY DIFFRACTIONf_dihedral_angle_d16.6291013
X-RAY DIFFRACTIONf_chiral_restr0.079389
X-RAY DIFFRACTIONf_plane_restr0.005539
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8488-1.90840.33481350.30282498263398
1.9084-1.97660.32851290.26652478260798
1.9766-2.05580.29151330.2542512264599
2.0558-2.14930.28781330.22492534266799
2.1493-2.26260.27731310.21122514264599
2.2626-2.40440.25651330.21282546267999
2.4044-2.590.28051340.20282537267199
2.59-2.85060.27241340.184325802714100
2.8506-3.26290.24621340.17382550268499
3.2629-4.11030.1771390.140726482787100
4.1103-40.53350.19721460.181127772923100

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