5A6K

GH20C, Beta-hexosaminidase from Streptococcus pneumoniae in complex with Gal-NGT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A Second Beta-Hexosaminidase Encoded in the Streptococcus Pneumoniae Genome Provides an Expanded Biochemical Ability to Degrade Host Glycans

Robb, M.Robb, C.S.Higgins, M.A.Hobbs, J.K.Paton, J.C.Boraston, A.B.

(2015) J Biol Chem 290: 30888

  • DOI: 10.1074/jbc.M115.688630
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An important facet of the interaction between the pathogen Streptococcus pneumoniae (pneumococcus) and its human host is the ability of this bacterium to process host glycans. To achieve cleavage of the glycosidic bonds in host glycans, S. pneumoniae ...

    An important facet of the interaction between the pathogen Streptococcus pneumoniae (pneumococcus) and its human host is the ability of this bacterium to process host glycans. To achieve cleavage of the glycosidic bonds in host glycans, S. pneumoniae deploys a wide array of glycoside hydrolases. Here, we identify and characterize a new family 20 glycoside hydrolase, GH20C, from S. pneumoniae. Recombinant GH20C possessed the ability to hydrolyze the β-linkages joining either N-acetylglucosamine or N-acetylgalactosamine to a wide variety of aglycon residues, thus revealing this enzyme to be a generalist N-acetylhexosaminidase in vitro. X-ray crystal structures were determined for GH20C in a ligand-free form, in complex with the N-acetylglucosamine and N-acetylgalactosamine products of catalysis and in complex with both gluco- and galacto-configured inhibitors O-(2-acetamido-2-deoxy-D-glucopyranosylidene)amino N-phenyl carbamate (PUGNAc), O-(2-acetamido-2-deoxy-D-galactopyranosylidene)amino N-phenyl carbamate (GalPUGNAc), N-acetyl-D-glucosamine-thiazoline (NGT), and N-acetyl-D-galactosamine-thiazoline (GalNGT) at resolutions from 1.84 to 2.7 Å. These structures showed N-acetylglucosamine and N-acetylgalactosamine to be recognized via identical sets of molecular interactions. Although the same sets of interaction were maintained with the gluco- and galacto-configured inhibitors, the inhibition constants suggested preferred recognition of the axial O4 when an aglycon moiety was present (Ki for PUGNAc > GalPUGNAc) but preferred recognition of an equatorial O4 when the aglycon was absent (Ki for GalNGT > NGT). Overall, this study reveals GH20C to be another tool that is unique in the arsenal of S. pneumoniae and that it may implement the effort of the bacterium to utilize and/or destroy the wide array of host glycans that it may encounter.


    Organizational Affiliation

    From the Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada V8W 3P6 and boraston@uvic.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GH20C
A, B
649Streptococcus pneumoniae TIGR4Mutation(s): 0 
Gene Names: SP_2141
EC: 3.2.1.52
Find proteins for A0A0H2US73 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2US73
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NSG
Query on NSG

Download CCD File 
A, B
(2S,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methyl-2,3a,5,6,7,7a-hexahydro-1H-pyrano[3,2-d][1,3]thiazole-6,7-diol
C8 H15 N O4 S
XWPUWEBFKDEDIF-JMHNFOGYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NSGKi:  1130   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.69α = 90
b = 99.42β = 90
c = 133.17γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-23
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references