1V0E | pdb_00001v0e

Endosialidase of Bacteriophage K1F

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.202 (Depositor) 
  • R-Value Work: 
    0.166 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

Crystal Structure of the Polysialic Acid-Degrading Endosialidase of Bacteriophage K1F

Stummeyer, K., Dickmanns, A., Muehlenhoff, M., Gerardy-Schahn, R., Ficner, R.

(2005) Nat Struct Mol Biol 12: 90

  • DOI: https://doi.org/10.1038/nsmb874
  • Primary Citation Related Structures: 
    1V0E, 1V0F

  • PubMed Abstract: 

    Phages infecting the polysialic acid (polySia)-encapsulated human pathogen Escherichia coli K1 are equipped with capsule-degrading tailspikes known as endosialidases, which are the only identified enzymes that specifically degrade polySia. As polySia also promotes cellular plasticity and tumor metastasis in vertebrates, endosialidases are widely applied in polySia-related neurosciences and cancer research. Here we report the crystal structures of endosialidase NF and its complex with oligomeric sialic acid. The structure NF, which reveals three distinct domains, indicates that the unique polySia specificity evolved from a combination of structural elements characteristic of exosialidases and bacteriophage tailspike proteins. The endosialidase assembles into a catalytic trimer stabilized by a triple beta-helix. Its active site differs markedly from that of exosialidases, indicating an endosialidase-specific substrate-binding mode and catalytic mechanism. Residues essential for endosialidase activity were identified by structure-based mutational analysis.

    • Organizational Affiliation: 
    • Abteilung Zelluläre Chemie, Zentrum Biochemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.

Macromolecule Content 

  • Total Structure Weight: 445.36 kDa 
  • Atom Count: 34,485 
  • Modeled Residue Count: 3,996 
  • Deposited Residue Count: 3,996 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ENDO-ALPHA-SIALIDASE
A, B, C, D, E
A, B, C, D, E, F
666Escherichia phage K1FMutation(s): 0 
EC: 3.2.1.129
UniProt
Find proteins for Q04830 (Escherichia phage K1F)
Explore Q04830 
Go to UniProtKB:  Q04830
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04830
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.202 (Depositor) 
  • R-Value Work:  0.166 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.65α = 90
b = 131.25β = 90
c = 346.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-13
    Type: Initial release
  • Version 1.1: 2011-06-02
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Other