6PHX

SpAga D472N structure in complex with raffinose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Molecular analysis of an enigmaticStreptococcus pneumoniaevirulence factor: The raffinose-family oligosaccharide utilization system.

Hobbs, J.K.Meier, E.P.W.Pluvinage, B.Mey, M.A.Boraston, A.B.

(2019) J.Biol.Chem. 294: 17197-17208

  • DOI: 10.1074/jbc.RA119.010280
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • <i>Streptococcus pneumoniae </i> is an opportunistic respiratory pathogen that can spread to other body sites, including the ears, brain and blood. The ability of this bacterium to breakdown, import and metabolize a wide range of glycans is key to i ...

    Streptococcus pneumoniae is an opportunistic respiratory pathogen that can spread to other body sites, including the ears, brain and blood. The ability of this bacterium to breakdown, import and metabolize a wide range of glycans is key to its virulence. Intriguingly, S. pneumoniae can utilize several plant oligosaccharides for growth in vitro , including raffinose-family oligosaccharides (RFOs, which are α-(1→6)-galactosyl extensions of sucrose). An RFO utilization locus has been identified in the pneumococcal genome; however, none of the proteins encoded by this locus have been biochemically characterized. The enigmatic ability of S. pneumoniae to utilize RFOs has recently received attention as mutations in two of the RFO locus genes have been linked to the tissue tropism of clinical pneumococcal isolates. Here, we use functional studies combined with X-ray crystallography to show that, while the pneumococcal RFO locus encodes for all the machinery required for uptake and degradation of RFOs, the individual pathway components are biochemically inefficient. We also demonstrate that the initiating enzyme in this pathway, the α-galactosidase Aga (a family 36 glycoside hydrolase), can cleave α-(1→3)-linked galactose units from a linear blood group antigen. We propose that the pneumococcal RFO pathway is an evolutionary relic that is not utilized in this streptococcal species and, as such, is under no selection pressure to maintain binding affinity and/or catalytic efficiency. We speculate that the apparent contribution of RFO utilization to pneumococcal tissue tropism may, in fact, be due to the essential role the ATPase RafK plays in the transport of other carbohydrates.


    Organizational Affiliation

    University of Victoria, Canada.,Biochemistry and Microbiology, University of Victoria, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alpha-galactosidase
A
740Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)Mutation(s): 1 
Gene Names: aga
EC: 3.2.1.22
Find proteins for A0A0H2URQ6 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Go to UniProtKB:  A0A0H2URQ6
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRU
Query on FRU

Download SDF File 
Download CCD File 
A
FRUCTOSE
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
 Ligand Interaction
ACT
Query on ACT

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

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Download CCD File 
A
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
GLC
Query on GLC

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Download CCD File 
A
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
GLA
Query on GLA

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Download CCD File 
A
ALPHA D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.191 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 91.027α = 90.00
b = 127.452β = 90.00
c = 151.955γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Database references
  • Version 1.2: 2019-11-27
    Type: Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence