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- PDB-2mze: NMR Solution Structure of the PRO Form of Human Matrilysin (proMMP-7) -

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Basic information

Entry
Database: PDB / ID: 2mze
TitleNMR Solution Structure of the PRO Form of Human Matrilysin (proMMP-7)
ComponentsMatrilysin
KeywordsHYDROLASE / zymogen / metalloenzyme
Function / homology
Function and homology information


matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / membrane protein ectodomain proteolysis / Collagen degradation / collagen catabolic process / extracellular matrix disassembly ...matrilysin / antibacterial peptide secretion / antibacterial peptide biosynthetic process / membrane protein intracellular domain proteolysis / Assembly of collagen fibrils and other multimeric structures / Activation of Matrix Metalloproteinases / membrane protein ectodomain proteolysis / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / metallopeptidase activity / regulation of cell population proliferation / defense response to Gram-negative bacterium / endopeptidase activity / Extra-nuclear estrogen signaling / defense response to Gram-positive bacterium / positive regulation of cell migration / response to xenobiotic stimulus / serine-type endopeptidase activity / proteolysis / extracellular space / zinc ion binding / extracellular exosome / extracellular region
Similarity search - Function
Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase ...Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Putative peptidoglycan binding domain / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model1
AuthorsPrior, S.H. / Fulcher, Y.G. / Van Doren, S.R.
CitationJournal: Structure / Year: 2015
Title: Charge-Triggered Membrane Insertion of Matrix Metalloproteinase-7, Supporter of Innate Immunity and Tumors.
Authors: Prior, S.H. / Fulcher, Y.G. / Koppisetti, R.K. / Jurkevich, A. / Van Doren, S.R.
History
DepositionFeb 11, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1245
Polymers27,9131
Non-polymers2114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Matrilysin / Matrin / Matrix metalloproteinase-7 / MMP-7 / Pump-1 protease / Uterine metalloproteinase


Mass: 27912.572 Da / Num. of mol.: 1 / Mutation: E195A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP7, MPSL1, PUMP1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09237, matrilysin
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D HNCO
1613D HNCA
1713D HN(CO)CA
1812D 1H-13C HSQC aromatic
1913D H(CCO)NH
11013D (H)CCH-TOCSY
1111(Hb)Cb(CgCd)Hd
1121(Hb)Cb(CgCd)He
11322D 1H-13C HSQC
11413D 1H-15N NOESY
11513D 1H-13C NOESY
11612D 1H-13C HSQC aromatic
11733D 1H-15N NOESY
11833D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.4 mM [U-100% 13C; U-100% 15N] proMMP-7(E195A), 20 mM imidazole, pH 6.6, 10 mM CaCl2, 20 uM ZnCl2, 10 mM beta-mercaptoethanol, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.4 mM [U-10% 13C; U-100% 15N] proMMP-7(E195A), 20 mM imidazole, pH 6.6, 10 mM CaCl2, 20 uM ZnCl2, 10 mM beta-mercaptoethanol, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.4 mM [U-100% 15N, U-100% 13CH3 (ILV)] proMMP-7(E195A), 20 mM imidazole, pH 6.6, 10 mM CaCl2, 20 uM ZnCl2, 10 mM beta-mercaptoethanol, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.4 mMproMMP-7(E195A)-1[U-100% 13C; U-100% 15N]1
20 mMimidazole, pH 6.6-21
10 mMCaCl2-31
20 uMZnCl2-41
10 mMbeta-mercaptoethanol-51
0.02 %sodium azide-61
0.4 mMproMMP-7(E195A)-7[U-10% 13C; U-100% 15N]2
20 mMimidazole, pH 6.6-82
10 mMCaCl2-92
20 uMZnCl2-102
10 mMbeta-mercaptoethanol-112
0.02 %sodium azide-122
0.4 mMproMMP-7(E195A)-13[U-100% 15N, U-100% 13CH3 (ILV)]3
20 mMimidazole, pH 6.6-143
10 mMCaCl2-153
20 uMZnCl2-163
10 mMbeta-mercaptoethanol-173
0.02 %sodium azide-183
Sample conditionspH: 6.6 / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1Bruker Biospincollection
TopSpin3.1Bruker Biospinprocessing
Analysis2.4CCPNpeak picking
Analysis2.4CCPNchemical shift assignment
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
PSVSBhattacharya and Montelionevalidation
CYANArefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsHydrogen bond constraints total count: 18
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.27 Å

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