4HIZ | pdb_00004hiz

Phage phi92 endosialidase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.147 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.107 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 
    0.107 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history. 


Literature

Structure and biochemical characterization of bacteriophage phi92 endosialidase.

Schwarzer, D., Browning, C., Stummeyer, K., Oberbeck, A., Muhlenhoff, M., Gerardy-Schahn, R., Leiman, P.G.

(2015) Virology 477: 133-143

  • DOI: https://doi.org/10.1016/j.virol.2014.11.002
  • Primary Citation of Related Structures:  
    4HIZ

  • PubMed Abstract: 

    Surface-associated capsular polysaccharides (CPSs) protect bacteria against phage infection and enhance pathogenicity by interfering with the function of the host innate immune system. The CPS of enteropathogenic Escherichia coli K92 is a unique sialic acid polymer (polySia) with alternating α2,8- and α2,9-linkages. This CPS can be digested by the gene 143 encoded endosialidase of bacteriophage phi92. Here we report the crystal structure of the phi92 endosialidase in complex with a dimer of α2,9-linked sialic acid and analyze its catalytic functions. Unlike the well characterized and homologous endosialidase of phage K1F, the phi92 endosialidase is a bifunctional enzyme with high activity against α2,8- and low activity against α2,9-linkages in a polySia chain. Moreover, in contrast to the processive K1F endosialidase, the phi92 endosialidase degrades the polymer in a non-processive mode. Beyond describing the first endosialidase with α2,9-specificity, our data introduce a novel platform for studies of endosialidase regioselectivity and for engineering highly active α2,9-specific enzymes.

    • Organizational Affiliation: 
    • Institute for Cellular Chemistry, Hannover Medical School (MHH), 30625 Hannover, Germany.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endosialidase
A, B, C
683Escherichia phage phi92Mutation(s): 0 
Gene Names: gene 143, PHI92_gene_143
EC: 3.2.1.129
UniProt
Find proteins for I7HXG2 (Escherichia phage phi92)
Explore I7HXG2 
Go to UniProtKB:  I7HXG2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI7HXG2
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-9)-N-acetyl-beta-neuraminic acid
D, E, F
2N/A
Glycosylation Resources
GlyTouCan:  G64530AY
GlyCosmos:  G64530AY
GlyGen:  G64530AY
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
G, H, I
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
BB [auth C]
CB [auth C]
DB [auth C]
EB [auth C]
FB [auth C]
BB [auth C],
CB [auth C],
DB [auth C],
EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C],
IB [auth C],
J [auth A],
JA [auth B],
JB [auth C],
K [auth A],
KA [auth B],
KB [auth C],
L [auth A],
LA [auth B],
LB [auth C],
M [auth A],
MA [auth B],
MB [auth C],
N [auth A],
NA [auth B],
NB [auth C],
O [auth A],
OA [auth B],
OB [auth C],
P [auth A],
PA [auth B],
Q [auth A],
QA [auth B],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
W [auth A],
X [auth A],
Y [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File 
CA [auth A]
DA [auth A]
QB [auth C]
RB [auth C]
YA [auth B]
CA [auth A],
DA [auth A],
QB [auth C],
RB [auth C],
YA [auth B],
ZA [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
AA [auth A],
BA [auth A],
PB [auth C],
XA [auth B]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
WA [auth B],
Z [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
AB [auth B]
EA [auth A]
FA [auth A]
GA [auth A]
HA [auth A]
AB [auth B],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
SB [auth C],
TB [auth C],
UB [auth C],
VB [auth C],
WB [auth C],
XB [auth C]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.147 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.107 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 0.107 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.858α = 90
b = 137.584β = 94.64
c = 140.778γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
AMoREphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RemDAqdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Derived calculations, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.2: 2025-04-16
    Changes: Database references, Structure summary