31591266, J Biol Chem. 2019 Nov 15;294(46):17197-17208. doi: 10.1074/jbc.RA119.010280. Epub 2019 Oct 7.

Characterization method

enzyme activity assay

Genomic accession number


Nucelotide position range







Streptococcus pneumoniae/1313

Degradation or Biosynthesis


Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- SP_1893 AAK75964.1 0 - 1194 (-) AE005672.3:1798266-1799460 -
gtfA SP_1894 AAK75965.1 1331 - 2774 (-) AE005672.3:1799597-1801040
rafG SP_1895 AAK75966.1 3131 - 3968 (-) AE005672.3:1801397-1802234 -
rafF SP_1896 AAK75967.1 3978 - 4869 (-) AE005672.3:1802244-1803135 -
rafE SP_1897 AAK75968.1 4858 - 6118 (-) AE005672.3:1803124-1804384 -
aga SP_1898 AAK75969.1 6209 - 8372 (-) AE005672.3:1804475-1806638
msmR SP_1899 AAK75970.1 8479 - 9337 (+) AE005672.3:1806745-1807603 -

Cluster number


Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1194 (-) TC: gnl|TC-DB|Q97NW6|9.B.67.1.2 Yes
gtfA 1332 - 2774 (-) CAZyme: GH13|GH13_18 Yes
rafG 3132 - 3968 (-) TC: gnl|TC-DB|Q00751|3.A.1.1.28 Yes
rafF 3979 - 4869 (-) TC: gnl|TC-DB|Q00750|3.A.1.1.28 Yes
rafE 4859 - 6118 (-) TC: gnl|TC-DB|Q00749|3.A.1.1.28 Yes
aga 6210 - 8372 (-) CDS No
msmR 8480 - 9337 (+) STP: STP|AraC_binding,STP|HTH_18 No




31591266, J Biol Chem. 2019 Nov 15;294(46):17197-17208. doi: 10.1074/jbc.RA119.010280. Epub 2019 Oct 7.


Molecular analysis of an enigmatic Streptococcus pneumoniae virulence factor: The raffinose-family oligosaccharide utilization system.


Hobbs JK, Meier EPW, Pluvinage B, Mey MA, Boraston AB


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 break down, 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 alpha-(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 because 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 although 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 alpha-galactosidase Aga (a family 36 glycoside hydrolase), can cleave alpha-(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.