3GVJ

Crystal structure of an endo-neuraminidaseNF mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the recognition and cleavage of polysialic acid by the bacteriophage K1F tailspike protein EndoNF.

Schulz, E.C.Schwarzer, D.Frank, M.Stummeyer, K.Muhlenhoff, M.Dickmanns, A.Gerardy-Schahn, R.Ficner, R.

(2010) J.Mol.Biol. 397: 341-351

  • DOI: 10.1016/j.jmb.2010.01.028
  • Primary Citation of Related Structures:  3GVK, 3GVL

  • PubMed Abstract: 
  • An alpha-2,8-linked polysialic acid (polySia) capsule confers immune tolerance to neuroinvasive, pathogenic prokaryotes such as Escherichia coli K1 and Neisseria meningitidis and supports host infection by means of molecular mimicry. Bacteriophages o ...

    An alpha-2,8-linked polysialic acid (polySia) capsule confers immune tolerance to neuroinvasive, pathogenic prokaryotes such as Escherichia coli K1 and Neisseria meningitidis and supports host infection by means of molecular mimicry. Bacteriophages of the K1 family, infecting E. coli K1, specifically recognize and degrade this polySia capsule utilizing tailspike endosialidases. While the crystal structure for the catalytic domain of the endosialidase of bacteriophage K1F (endoNF) has been solved, there is yet no structural information on the mode of polySia binding and cleavage available. The crystal structure of activity deficient active-site mutants of the homotrimeric endoNF cocrystallized with oligomeric sialic acid identified three independent polySia binding sites in each endoNF monomer. The bound oligomeric sialic acid displays distinct conformations at each site. In the active site, a Sia(3) molecule is bound in an extended conformation representing the enzyme-product complex. Structural and biochemical data supported by molecular modeling enable to propose a reaction mechanism for polySia cleavage by endoNF.


    Organizational Affiliation

    Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Endo-N-acetylneuraminidase
A
670Enterobacteria phage K1FEC: 3.2.1.129
Find proteins for Q04830 (Enterobacteria phage K1F)
Go to UniProtKB:  Q04830
Small Molecules
Ligands 2 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
SIA
Query on SIA

Download SDF File 
Download CCD File 
A
O-SIALIC ACID
C11 H19 N O9
SQVRNKJHWKZAKO-YRMXFSIDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 119.090α = 90.00
b = 119.090β = 90.00
c = 175.980γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-03-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance