Agarose and porphyran are related galactans that are only found within red marine algae. As such, marine microorganisms have adapted to using these polysaccharides as carbon sources through the acquisition of unique Carbohydrate Active enZymes (CAZymes). A recent metagenome study of the microbiomes from a Japanese human population identified putative CAZymes in several bacterial species, including Bacteroides plebeius that have significant amino acid sequence similarity with those from marine bacteria. Analysis of one potential CAZyme from B. plebeius (BpGH50) is described here. While displaying up to 30% sequence identity with β-agarases, BpGH50 has no detectable agarase activity. Its crystal structure reveals that the topology of the active site is much different than previously characterized agarases, while containing the same core catalytic machinery. It is unclear whether the enzyme has endo- or exo- activity; the large binding ‘groove’ is typical of an endo-acting enzyme, while a loop at one end of the groove may provide a terminal pocket for the substrate, which is suggestive of exo-activity. Furthermore, the enzyme contains a basic pocket that may dock a sulphated substrate, like porphyran. While no quantifiable porphyran activity was observed, properties of the putative active site suggest that this unusual enzyme may be specific on an unusual substrate, such as a porphyran-agarose hybrid. / Graduate
| Identifer | oai:union.ndltd.org:uvic.ca/oai:dspace.library.uvic.ca:1828/5832 |
| Date | 02 January 2015 |
| Creators | Giles, Kaleigh |
| Contributors | Boraston, Alisdair Bennett |
| Source Sets | University of Victoria |
| Language | English, English |
| Detected Language | English |
| Type | Thesis |
| Rights | Available to the World Wide Web |
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