5DHM

Crystal structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structure of the fimbrial protein Mfa4 from Porphyromonas gingivalis in its precursor form: implications for a donor-strand complementation mechanism.

Kloppsteck, P.Hall, M.Hasegawa, Y.Persson, K.

(2016) Sci Rep 6: 22945-22945

  • DOI: https://doi.org/10.1038/srep22945
  • Primary Citation of Related Structures:  
    5DHM

  • PubMed Abstract: 

    Gingivitis and periodontitis are chronic inflammatory diseases that can lead to tooth loss. One of the causes of these diseases is the Gram-negative Porphyromonas gingivalis. This periodontal pathogen is dependent on two fimbriae, FimA and Mfa1, for binding to dental biofilm, salivary proteins, and host cells. These fimbriae are composed of five proteins each, but the fimbriae assembly mechanism and ligands are unknown. Here we reveal the crystal structure of the precursor form of Mfa4, one of the accessory proteins of the Mfa1 fimbria. Mfa4 consists of two β-sandwich domains and the first part of the structure forms two well-defined β-strands that run over both domains. This N-terminal region is cleaved by gingipains, a family of proteolytic enzymes that encompass arginine- and lysine-specific proteases. Cleavage of the N-terminal region generates the mature form of the protein. Our structural data allow us to propose that the new N-terminus of the mature protein may function as a donor strand in the polymerization of P. gingivalis fimbriae.


  • Organizational Affiliation

    Department of Chemistry, Umeå University, Umeå, SE-901 87, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoreactive 32 kDa antigenA,
C [auth B]
53Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_0290
UniProt
Find proteins for B2RHG4 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RHG4 
Go to UniProtKB:  B2RHG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RHG4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Immunoreactive 32 kDa antigenB [auth C],
D
282Porphyromonas gingivalis ATCC 33277Mutation(s): 0 
Gene Names: PGN_0290
UniProt
Find proteins for B2RHG4 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561))
Explore B2RHG4 
Go to UniProtKB:  B2RHG4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2RHG4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
C [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.683α = 90
b = 84.536β = 90
c = 138.364γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2011-4186
Umea Centre for Microbial ResearchSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release