2PYB

Napa protein from borrelia burgdorferi

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structure and immunomodulatory property relationship in NapA of Borrelia burgdorferi.

Codolo, G., Papinutto, E., Polenghi, A., D'Elios, M.M., Zanotti, G., de Bernard, M.

(2010) Biochim.Biophys.Acta 1804: 2191-2197

  • DOI: 10.1016/j.bbapap.2010.09.004

  • PubMed Abstract: 

    • NapA from Borrelia burgdorferi is a member of the Dps-like protein family with specific immunomodulatory properties; in particular, NapA is able to induce the expression of IL-23 in neutrophils and monocytes, as well as the expression of IL-6, IL-1β, ...

    NapA from Borrelia burgdorferi is a member of the Dps-like protein family with specific immunomodulatory properties; in particular, NapA is able to induce the expression of IL-23 in neutrophils and monocytes, as well as the expression of IL-6, IL-1β, and transforming growth factor beta (TGF-β) in monocytes, via Toll-like receptor (TLR) 2. Such an activity on innate immune cells triggers a synovial fluid Th17 response. Here we report the crystal structure of NapA, determined at 2.6Å resolution, which shows that the quaternary structure of the protein is that of a dodecamer with 23 symmetry, typical of the proteins of the family. We also demonstrate that the N- and C-terminal tails, which are flexible and not visible in the crystal, are not relevant for its pro-Th17 activity. Based on the crystal structure and on the comparison with the structure of the orthologous protein from Helicobacter pylori, HP-NAP, we hypothesize that the charge distributions on the two proteins' surfaces are responsible for the interaction with TLR2 and for the different behaviors in modulating the immune response.

    Related Citations: 
    • The Dodecameric Ferritin from Listeria Innocua Contains a Novel Intersubunit Iron Binding Site
      Ilari, A.,Stefanini, S.,Chiancone, E.,Tsernoglou, D.
      (2000) Nat.Struct.Mol.Biol. 7: 38
    • The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA
      Grant, R.A.,Filman, D.J.,Finkel, S.E.,Kolter, R.,Hogle, J.M.
      (1998) Nat.Struct.Mol.Biol. 5: 294
    • Structure of the neutrophil-activating protein from Helicobacter pylori
      Zanotti, G.,Papinutto, E.,Dundon, W.,Battistutta, R.,Seveso, M.,Dal Giudice, G.,Montecucco, C.
      (2002) J.Mol.Biol. 323: 125

    Organizational Affiliation: 

    Venetian Institute of Molecular Medicine, Via Orus 2, 35129 Padua, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil activating protein
A, B, C, D
151Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680)Mutation(s): 0 
Gene Names: napA
Find proteins for O51633 (Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680))
Go to UniProtKB:  O51633
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE
Download SDF File 
Download CCD File 
A, B, C, D
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.242 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 93.078α = 90.00
b = 93.078β = 90.00
c = 227.500γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
MAR345dtbdata collection
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2016-10-26
    Type: Database references