4MNP

Structure of the Sialic Acid Binding Protein from Fusobacterium Nucleatum subsp. nucleatum ATCC 25586


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site.

Gangi Setty, T.Cho, C.Govindappa, S.Apicella, M.A.Ramaswamy, S.

(2014) Acta Crystallogr.,Sect.D 70: 1801-1811

  • DOI: 10.1107/S139900471400830X
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the ho ...

    Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.


    Related Citations: 
    • Characterization of the N-acetyl-5-neuraminic acid-binding site of the extracytoplasmic solute receptor (SiaP) of nontypeable Haemophilus influenzae strain 2019.
      Johnston, J.W.,Coussens, N.P.,Allen, S.,Houtman, J.C.,Turner, K.H.,Zaleski, A.,Ramaswamy, S.,Gibson, B.W.,Apicella, M.A.
      (2008) J.Biol.Chem. 283: 855


    Organizational Affiliation

    Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-acetylneuraminate-binding protein
A
312Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131)Mutation(s): 0 
Find proteins for Q8RDN9 (Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / CIP 101130 / JCM 8532 / LMG 13131))
Go to UniProtKB:  Q8RDN9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SLB
Query on SLB

Download SDF File 
Download CCD File 
A
5-N-ACETYL-BETA-D-NEURAMINIC ACID
BETA-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-PFQGKNLYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SLBKd: 45.5 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.841α = 90.00
b = 58.729β = 90.00
c = 111.671γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references