5NCW

Structure of the trypsin induced serpin-type proteinase inhibitor, miropin (V367K/K368A mutant).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A structure-derived snap-trap mechanism of a multispecific serpin from the dysbiotic human oral microbiome.

Goulas, T.Ksiazek, M.Garcia-Ferrer, I.Sochaj-Gregorczyk, A.M.Waligorska, I.Wasylewski, M.Potempa, J.Gomis-Ruth, F.X.

(2017) J. Biol. Chem. 292: 10883-10898

  • DOI: 10.1074/jbc.M117.786533
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enduring host-microbiome relationships are based on adaptive strategies within a particular ecological niche. Tannerella forsythia is a dysbiotic member of the human oral microbiome that inhabits periodontal pockets and contributes to chronic periodo ...

    Enduring host-microbiome relationships are based on adaptive strategies within a particular ecological niche. Tannerella forsythia is a dysbiotic member of the human oral microbiome that inhabits periodontal pockets and contributes to chronic periodontitis. To counteract endopeptidases from the host or microbial competitors, T. forsythia possesses a serpin-type proteinase inhibitor called miropin. Although serpins from animals, plants, and viruses have been widely studied, those from prokaryotes have received only limited attention. Here we show that miropin uses the serpin-type suicidal mechanism. We found that, similar to a snap trap, the protein transits from a metastable native form to a relaxed triggered or induced form after cleavage of a reactive-site target bond in an exposed reactive-center loop. The prey peptidase becomes covalently attached to the inhibitor, is dragged 75 Å apart, and is irreversibly inhibited. This coincides with a large conformational rearrangement of miropin, which inserts the segment upstream of the cleavage site as an extra β-strand in a central β-sheet. Standard serpins possess a single target bond and inhibit selected endopeptidases of particular specificity and class. In contrast, miropin uniquely blocked many serine and cysteine endopeptidases of disparate architecture and substrate specificity owing to several potential target bonds within the reactive-center loop and to plasticity in accommodating extra β-strands of variable length. Phylogenetic studies revealed a patchy distribution of bacterial serpins incompatible with a vertical descent model. This finding suggests that miropin was acquired from the host through horizontal gene transfer, perhaps facilitated by the long and intimate association of T. forsythia with the human gingiva.


    Organizational Affiliation

    From the Proteolysis Lab, Structural Biology Unit, María de Maeztu Unit of Excellence, Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas, 08028 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serpin-type proteinase inhibitor, miropin
A
334Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338)Mutation(s): 1 
Find proteins for G8UQY8 (Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338))
Go to UniProtKB:  G8UQY8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serpin-type proteinase inhibitor, miropin
B
41Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338)Mutation(s): 1 
Find proteins for G8UQY8 (Tannerella forsythia (strain ATCC 43037 / JCM 10827 / FDC 338))
Go to UniProtKB:  G8UQY8
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 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
TRS
Query on TRS

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A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 62.600α = 90.00
b = 74.280β = 90.00
c = 84.380γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement
PHENIXrefinement
BUSTERrefinement
Cootmodel building
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionSpainFP7-HEALTH-2012-306029-2
Spanish Ministry of Economy and CompetitivenessSpainBFU2015-64487-R
Spanish Ministry of Economy and CompetitivenessSpainBIO2013-49320-EXP
Spanish Ministry of Economy and CompetitivenessSpainMDM-2014-0435
Catalan GovernmentSpainJCI-2012-13573
Spanish Ministry of Economy and CompetitivenessSpain2014SGR9

Revision History 

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2017-07-12
    Type: Database references
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence