2PYB

Napa protein from borrelia burgdorferi

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.242 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    2PYB

  • 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, and transforming growth factor beta (TGF-β) in monocytes, via Toll-like receptor (TLR) 2 ...

    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: 
    • 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
    • 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
    • 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
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil activating proteinA, B, C, D151N/AMutation(s): 0 
Gene Names: NAPA
UniProt
Find proteins for O51633 (Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680))
Explore O51633 
Go to UniProtKB:  O51633
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO51633
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.242 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.078α = 90
b = 93.078β = 90
c = 227.5γ = 120
Software Package:
Software NamePurpose
CNSrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

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