6OR4

Crystal structure of SpGH29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Two complementary alpha-fucosidases fromStreptococcus pneumoniaepromote complete degradation of host-derived carbohydrate antigens.

Hobbs, J.K.Pluvinage, B.Robb, M.Smith, S.P.Boraston, A.B.

(2019) J Biol Chem 294: 12670-12682

  • DOI: 10.1074/jbc.RA119.009368
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An important aspect of the interaction between the opportunistic bacterial pathogen Streptococcus pneumoniae and its human host is its ability to harvest host glycans. The pneumococcus can degrade a variety of complex glycans, including ...

    An important aspect of the interaction between the opportunistic bacterial pathogen Streptococcus pneumoniae and its human host is its ability to harvest host glycans. The pneumococcus can degrade a variety of complex glycans, including N - and O -linked glycans, glycosaminoglycans, and carbohydrate antigens, an ability that is tightly linked to the virulence of S. pneumoniae Although S. pneumoniae is known to use a sophisticated enzyme machinery to attack the human glycome, how it copes with fucosylated glycans, which are primarily histo-blood group antigens, is largely unknown. Here, we identified two pneumococcal enzymes, Sp GH29 C and Sp GH95 C , that target α-(1→3/4) and α-(1→2) fucosidic linkages, respectively. X-ray crystallography studies combined with functional assays revealed that Sp GH29 C is specific for the Lewis A and Lewis X antigen motifs and that Sp GH95 C is specific for the H(O)-antigen motif. Together, these enzymes could defucosylate Lewis Y and Lewis B antigens in a complementary fashion. In vitro reconstruction of glycan degradation cascades disclosed that the individual or combined activities of these enzymes expose the underlying glycan structure, promoting the complete deconstruction of a glycan that would otherwise be resistant to pneumococcal enzymes. These experiments expand our understanding of the extensive capacity of S. pneumoniae to process host glycans and the likely roles of α-fucosidases in this. Overall, given the importance of enzymes that initiate glycan breakdown in pneumococcal virulence, such as the neuraminidase NanA and the mannosidase Sp GH92, we anticipate that the α-fucosidases identified here will be important factors in developing more refined models of the S. pneumoniae -host interaction.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia V8P 5C2, Canada boraston@uvic.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycoside hydrolase
A, B
451Streptococcus pneumoniae TIGR4Mutation(s): 2 
Gene Names: SP_2146
Find proteins for A0A0H2US78 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2US78
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GAL
Query on GAL

Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.172 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.96α = 76.58
b = 68.82β = 73.24
c = 72.67γ = 73.61
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History 

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-04
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence, Data collection