6S0F

Crystal structure of an inverting family GH156 exosialidase from uncultured bacterium pG7 in complex with 3-Deoxy-D-glycero-D-galacto-2-nonulosonic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Inverting family GH156 sialidases define an unusual catalytic motif for glycosidase action.

Bule, P.Chuzel, L.Blagova, E.Wu, L.Gray, M.A.Henrissat, B.Rapp, E.Bertozzi, C.R.Taron, C.H.Davies, G.J.

(2019) Nat Commun 10: 4816-4816

  • DOI: 10.1038/s41467-019-12684-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sialic acids are a family of related sugars that play essential roles in many biological events intimately linked to cellular recognition in both health and disease. Sialidases are therefore orchestrators of cellular biology and important therapeutic ...

    Sialic acids are a family of related sugars that play essential roles in many biological events intimately linked to cellular recognition in both health and disease. Sialidases are therefore orchestrators of cellular biology and important therapeutic targets for viral infection. Here, we sought to define if uncharacterized sialidases would provide distinct paradigms in sialic acid biochemistry. We show that a recently discovered sialidase family, whose first member EnvSia156 was isolated from hot spring metagenomes, defines an unusual structural fold and active centre constellation, not previously described in sialidases. Consistent with an inverting mechanism, EnvSia156 reveals a His/Asp active center in which the His acts as a Brønsted acid and Asp as a Brønsted base in a single-displacement mechanism. A predominantly hydrophobic aglycone site facilitates accommodation of a variety of 2-linked sialosides; a versatility that offers the potential for glycan hydrolysis across a range of biological and technological platforms.


    Organizational Affiliation

    New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA.,New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA. taron@neb.com.,glyXera GmbH, Leipziger Strasse 44-ZENIT, Magdeburg, Germany.,Department of Chemistry, University of York, York, YO10 5DD, UK. gideon.davies@york.ac.uk.,Department of Chemistry, Stanford University, Stanford, CA, 94305-4404, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305-4404, USA.,Department of Chemistry, University of York, York, YO10 5DD, UK.,Architecture et Fonction des Macromolécules Biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS, UMR7257), Institut National Agronomique (INRA, USC 1408) and Aix-Marseille Université (AMU), 13288 Marseille cedex 9, Marseille, France.,Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106, Magdeburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
exosialidase from uncultured bacterium pG7
A, B
511N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SCN
Query on SCN

Download SDF File 
Download CCD File 
A, B
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
KDN
Query on KDN

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Download CCD File 
A, B
3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid
C9 H16 O9
CLRLHXKNIYJWAW-YOQZMRDMSA-N
 Ligand Interaction
TRS
Query on TRS

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Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 63.661α = 90.00
b = 78.924β = 94.89
c = 112.992γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
REFMACrefinement
PHASERphasing
DIALSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Royal SocietyUnited Kingdom--

Revision History 

  • Version 1.0: 2019-11-06
    Type: Initial release