5EDF

Crystal structure of the selenomethionine-substituted iron-regulated protein FrpD from Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitidis.

Sviridova, E.Rezacova, P.Bondar, A.Veverka, V.Novak, P.Schenk, G.Svergun, D.I.Kuta Smatanova, I.Bumba, L.

(2017) Sci Rep 7: 40408-40408

  • DOI: https://doi.org/10.1038/srep40408
  • Primary Citation of Related Structures:  
    5EDF, 5EDJ

  • PubMed Abstract: 

    The iron-regulated protein FrpD from Neisseria meningitidis is an outer membrane lipoprotein that interacts with very high affinity (K d  ~ 0.2 nM) with the N-terminal domain of FrpC, a Type I-secreted protein from the Repeat in ToXin (RTX) protein family. In the presence of Ca 2+ , FrpC undergoes Ca 2+ -dependent protein trans-splicing that includes an autocatalytic cleavage of the Asp 414 -Pro 415 peptide bond and formation of an Asp 414 -Lys isopeptide bond. Here, we report the high-resolution structure of FrpD and describe the structure-function relationships underlying the interaction between FrpD and FrpC 1-414 . We identified FrpD residues involved in FrpC 1-414 binding, which enabled localization of FrpD within the low-resolution SAXS model of the FrpD-FrpC 1-414 complex. Moreover, the trans-splicing activity of FrpC resulted in covalent linkage of the FrpC 1-414 fragment to plasma membrane proteins of epithelial cells in vitro, suggesting that formation of the FrpD-FrpC 1-414 complex may be involved in the interaction of meningococci with the host cell surface.


  • Organizational Affiliation

    Faculty of Science, University of South Bohemia Ceske Budejovice, Branisovska 1760, 37005 Ceske Budejovice, Czech Republic.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FrpC operon protein244Neisseria meningitidisMutation(s): 0 
Gene Names: LA50_03295
UniProt
Find proteins for Q08840 (Neisseria meningitidis)
Explore Q08840 
Go to UniProtKB:  Q08840
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08840
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.293α = 90
b = 38.829β = 90
c = 165.67γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Grant AgencyCzech RepublicP207/11/0717

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references