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- PDB-8b2n: Potempin A (PotA) from Tannerella forsythia in complex with the c... -

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Basic information

Entry
Database: PDB / ID: 8b2n
TitlePotempin A (PotA) from Tannerella forsythia in complex with the catalytic domain of human MMP-12
Components
  • Macrophage metalloelastase
  • Tannerella forsythia potempin A (PotA)
KeywordsHYDROLASE INHIBITOR / Metallopeptidase inhibitor
Function / homology
Function and homology information


macrophage elastase / negative regulation of endothelial cell-matrix adhesion / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development ...macrophage elastase / negative regulation of endothelial cell-matrix adhesion / bronchiole development / positive regulation of epithelial cell proliferation involved in wound healing / elastin catabolic process / regulation of defense response to virus by host / positive regulation of type I interferon-mediated signaling pathway / wound healing, spreading of epidermal cells / negative regulation of type I interferon-mediated signaling pathway / lung alveolus development / response to amyloid-beta / Collagen degradation / collagen catabolic process / positive regulation of interferon-alpha production / extracellular matrix disassembly / core promoter sequence-specific DNA binding / collagen binding / Degradation of the extracellular matrix / extracellular matrix organization / extracellular matrix / metalloendopeptidase activity / cellular response to virus / protein import into nucleus / endopeptidase activity / sequence-specific DNA binding / serine-type endopeptidase activity / calcium ion binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / proteolysis / extracellular space / extracellular region / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain ...Hemopexin, conserved site / Hemopexin domain signature. / Hemopexin-like domain / Peptidoglycan binding-like / Peptidase M10A, cysteine switch, zinc binding site / Matrixins cysteine switch. / Hemopexin-like repeats / Hemopexin-like domain superfamily / Hemopexin / Putative peptidoglycan binding domain / Hemopexin repeat profile. / Hemopexin-like repeats. / Peptidase M10A / Peptidase M10A, catalytic domain / Peptidase M10, metallopeptidase / Matrixin / PGBD-like superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Lipoprotein / Macrophage metalloelastase
Similarity search - Component
Biological speciesHomo sapiens (human)
Tannerella forsythia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPotempa, J. / Ksiazek, M. / Goulas, T. / Cuppari, A. / Rodriguez-Banqueri, A. / Arolas, J.L. / Lopez-Pelegrin, M. / Garcia-Ferrer, I. / Guevara, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Chem Sci / Year: 2023
Title: A unique network of attack, defence and competence on the outer membrane of the periodontitis pathogen Tannerella forsythia.
Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. ...Authors: Ksiazek, M. / Goulas, T. / Mizgalska, D. / Rodriguez-Banqueri, A. / Eckhard, U. / Veillard, F. / Waligorska, I. / Benedyk-Machaczka, M. / Sochaj-Gregorczyk, A.M. / Madej, M. / Thogersen, I.B. / Enghild, J.J. / Cuppari, A. / Arolas, J.L. / de Diego, I. / Lopez-Pelegrin, M. / Garcia-Ferrer, I. / Guevara, T. / Dive, V. / Zani, M.L. / Moreau, T. / Potempa, J. / Gomis-Ruth, F.X.
#1: Journal: Front Microbiol / Year: 2015
Title: KLIKK proteases of Tannerella forsythia: putative virulence factors with a unique domain structure.
Authors: Ksiazek, M. / Mizgalska, D. / Eick, S. / Thogersen, I.B. / Enghild, J.J. / Potempa, J.
History
DepositionSep 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Macrophage metalloelastase
B: Tannerella forsythia potempin A (PotA)
C: Macrophage metalloelastase
D: Tannerella forsythia potempin A (PotA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,99014
Polymers56,4874
Non-polymers50210
Water4,972276
1
A: Macrophage metalloelastase
B: Tannerella forsythia potempin A (PotA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4957
Polymers28,2442
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-72 kcal/mol
Surface area12040 Å2
MethodPISA
2
C: Macrophage metalloelastase
D: Tannerella forsythia potempin A (PotA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4957
Polymers28,2442
Non-polymers2515
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-73 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.410, 63.000, 135.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Macrophage metalloelastase / MME / Macrophage elastase / hME / Matrix metalloproteinase-12 / MMP-12


Mass: 17484.475 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MMP12, HME / Production host: Escherichia coli (E. coli) / References: UniProt: P39900, macrophage elastase
#2: Protein Tannerella forsythia potempin A (PotA)


Mass: 10759.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tannerella forsythia (bacteria) / Gene: CLI86_08900 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2A6E6U9
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The PotA:MMP-12 complex at 8.5 mg/mL in 2.5 mM calcium chloride, 150 mM sodium chloride, 20 mM Tris-HCl pH 7.5 was crystallised from 30% (w/v) PEG 3,000, 200 mM sodium chloride, 100 mM Tris-HCl pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.85→67.7 Å / Num. obs: 40486 / % possible obs: 99.9 % / Redundancy: 10.5 % / Biso Wilson estimate: 36.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.102 / Net I/σ(I): 14.3
Reflection shellResolution: 1.85→1.96 Å / Rmerge(I) obs: 0.835 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 6285 / CC1/2: 0.9 / Rrim(I) all: 0.878 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JK3

1jk3


Resolution: 1.85→67.69 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.136
RfactorNum. reflection% reflectionSelection details
Rfree0.228 798 1.97 %RANDOM
Rwork0.19 ---
obs0.19 40484 99.8 %-
Displacement parametersBiso mean: 40.97 Å2
Baniso -1Baniso -2Baniso -3
1-6.3973 Å20 Å20 Å2
2--8.1181 Å20 Å2
3----14.5154 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: 1 / Resolution: 1.85→67.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 10 276 4233
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094046HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.995482HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1823SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes684HARMONIC5
X-RAY DIFFRACTIONt_it4046HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion2.81
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion536SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance52HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4945SEMIHARMONIC4
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2657 -1.66 %
Rwork0.2549 2849 -
all0.255 2897 -
obs--98.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1261-1.26890.25483.957-0.43881.83280.26180.23320.0512-0.3423-0.18680.11550.0024-0.0535-0.075-0.0310.03370.02350.03060.0391-0.050511.1011-12.257-30.0813
23.9020.9735-0.87452.28790.45210.386-0.0338-0.15060.1931-0.23960.2239-0.395-0.13440.1005-0.19010.0111-0.0370.070.1005-0.03020.231237.2822-11.0538-27.1046
32.9116-0.2980.30153.81770.77112.16730.03160.0455-0.327-0.063-0.09830.57830.1271-0.08490.0668-0.03980.0032-0.02530.0108-0.04490.0235-28.9863-2.1409-61.7988
44.0025-0.3494-0.75032.59750.49251.7793-0.09990.1058-0.13890.03950.2461-0.39710.15270.2106-0.1462-0.00970.0484-0.02610.1256-0.0944-0.034-2.0581-1.3928-59.1478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|106 - 263 A|301 - 305 A|479 A|475 A|413 A|427}
2X-RAY DIFFRACTION2{B|27 - 118 }
3X-RAY DIFFRACTION3{C|106 - 263 C|301 - 305 C|463 C|450 C|406 C|419}
4X-RAY DIFFRACTION4{D|24 - 118 }

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