User:Wade Abbott

Dr. Abbott received his PhD from the University of Victoria in 2005. He then studied the molecular basis of protein-carbohydrate interactions under Dr. Alisdair Boraston at the University of Victoria. In 2008, Dr. Abbott joined Dr. Harry Gilbert's group at the Complex Carbohydrate Research Centre, at the University of Georgia where he investigated the functional genomics of carbohydrate utilization pathways from intestinal bacteria. Currently, Dr. Abbott is a Research Scientist for AAFC based at the Lethbridge Research Centre and Adjunct Professor at the University of Lethbridge. His research program investigates the mechanisms of complex carbohydrate modification by intestinal bacteria, and is developing applications for carbohydrates in animal agriculture and human intestinal health. See Abbott Group and Abbott Google Scholar for more information on research activities.

Dr. Abbott has contributed to structure-function studies of the following CAZyme Families:

Glycoside Hydrolases

• GH20 Streptococcus pneumoniae exo-β-D-N-acetylglucosaminidase (SpnGH20AB/StrH) [1, 2].

• GH28 Yersinia enterocolitica exopolygalacturonase (YeGH28) [3]. *Family First

• GH85 Streptococcus pneumoniae endo-β-D-glucosaminidase D (SpGH85/EndoD) [4]. *Family First

Polysaccharide Lyases

• PL2 Yersinia enterocolitica perplasmic pectate lyase (YePL2A) [5]. Paenibacillus sp. Y412MC10 Cytoplasmic endolytic pectate lyase (PaePL2) [6]. *Family First. Vibrio vulnificus sp. YJ016 endolytic pectate lyase (VvPL2) [7].
• PL22 Yersinia enterocolitica Cytoplasmic oligogalacturonate lyase (YePL22/Ogl) [8]. *Family First

Carbohydrate Binding Modules

• CBM6 [9, 10]
• CBM32 Yersinia enterocolitica polygalacturonic acid binding protein (YeCBM32) [11]. Streptococcus pneumoniae EndoD CBM (SpnCBM32) [12].
• CBM35 [10, 13]
• CBM51 Clostridium perfringens blood group binding CBMs (GH95CBM51 and GH98CBM51) [14]

Carbohydrate Esterases

• CE8 Yersinia enterocolitica pectin methylesterase [15]

Glycosyl Transferase

• GT32 Bacteroides thetaiotaomicron VPI-5482 α-1,3-mannosyltransferase (BT3775), α-1,6-mannosyltransferase (BT3776) [16]

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References

1. Pluvinage B, Chitayat S, Ficko-Blean E, Abbott DW, Kunjachen JM, Grondin J, Spencer HL, Smith SP, and Boraston AB. (2013). Conformational analysis of StrH, the surface-attached exo-β-D-N-acetylglucosaminidase from Streptococcus pneumoniae. J Mol Biol. 2013;425(2):334-49. DOI:10.1016/j.jmb.2012.11.005 |
2. Pluvinage B, Higgins MA, Abbott DW, Robb C, Dalia AB, Deng L, Weiser JN, Parsons TB, Fairbanks AJ, Vocadlo DJ, and Boraston AB. (2011). Inhibition of the pneumococcal virulence factor StrH and molecular insights into N-glycan recognition and hydrolysis. Structure. 2011;19(11):1603-14. DOI:10.1016/j.str.2011.08.011 |
3. Abbott DW and Boraston AB. (2007). The structural basis for exopolygalacturonase activity in a family 28 glycoside hydrolase. J Mol Biol. 2007;368(5):1215-22. DOI:10.1016/j.jmb.2007.02.083 |
4. Abbott DW, Macauley MS, Vocadlo DJ, and Boraston AB. (2009). Streptococcus pneumoniae endohexosaminidase D, structural and mechanistic insight into substrate-assisted catalysis in family 85 glycoside hydrolases. J Biol Chem. 2009;284(17):11676-89. DOI:10.1074/jbc.M809663200 |
5. Abbott DW and Boraston AB. (2007). A family 2 pectate lyase displays a rare fold and transition metal-assisted beta-elimination. J Biol Chem. 2007;282(48):35328-36. DOI:10.1074/jbc.M705511200 |
6. Abbott DW, Thomas D, Pluvinage B, and Boraston AB. (2013). An ancestral member of the polysaccharide lyase family 2 displays endolytic activity and magnesium dependence. Appl Biochem Biotechnol. 2013;171(7):1911-23. DOI:10.1007/s12010-013-0483-9 |
7. McLean R, Hobbs JK, Suits MD, Tuomivaara ST, Jones DR, Boraston AB, and Abbott DW. (2015). Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2. J Biol Chem. 2015;290(35):21231-43. DOI:10.1074/jbc.M115.664847 |
8. Abbott DW, Gilbert HJ, and Boraston AB. (2010). The active site of oligogalacturonate lyase provides unique insights into cytoplasmic oligogalacturonate beta-elimination. J Biol Chem. 2010;285(50):39029-38. DOI:10.1074/jbc.M110.153981 |
9. Abbott DW, Macauley MS, Vocadlo DJ, and Boraston AB. (2009). Streptococcus pneumoniae endohexosaminidase D, structural and mechanistic insight into substrate-assisted catalysis in family 85 glycoside hydrolases. J Biol Chem. 2009;284(17):11676-89. DOI:10.1074/jbc.M809663200 |
10. Abbott DW and van Bueren AL. (2014). Using structure to inform carbohydrate binding module function. Curr Opin Struct Biol. 2014;28:32-40. DOI:10.1016/j.sbi.2014.07.004 |
11. Abbott DW, Hrynuik S, and Boraston AB. (2007). Identification and characterization of a novel periplasmic polygalacturonic acid binding protein from Yersinia enterolitica. J Mol Biol. 2007;367(4):1023-33. DOI:10.1016/j.jmb.2007.01.030 |
12. Abbott DW and Boraston A. (2011). Structural analysis of a putative family 32 carbohydrate-binding module from the Streptococcus pneumoniae enzyme EndoD. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67(Pt 4):429-33. DOI:10.1107/S1744309111001874 |
13. Correia MA, Abbott DW, Gloster TM, Fernandes VO, Prates JA, Montanier C, Dumon C, Williamson MP, Tunnicliffe RB, Liu Z, Flint JE, Davies GJ, Henrissat B, Coutinho PM, Fontes CM, and Gilbert HJ. (2010). Signature active site architectures illuminate the molecular basis for ligand specificity in family 35 carbohydrate binding module. Biochemistry. 2010;49(29):6193-205. DOI:10.1021/bi1006139 |
14. Gregg KJ, Finn R, Abbott DW, and Boraston AB. (2008). Divergent modes of glycan recognition by a new family of carbohydrate-binding modules. J Biol Chem. 2008;283(18):12604-13. DOI:10.1074/jbc.M709865200 |
15. Boraston AB and Abbott DW. (2012). Structure of a pectin methylesterase from Yersinia enterocolitica. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68(Pt 2):129-33. DOI:10.1107/S1744309111055400 |
17. Cuskin F, Lowe EC, Temple MJ, Zhu Y, Cameron E, Pudlo NA, Porter NT, Urs K, Thompson AJ, Cartmell A, Rogowski A, Hamilton BS, Chen R, Tolbert TJ, Piens K, Bracke D, Vervecken W, Hakki Z, Speciale G, Munōz-Munōz JL, Day A, Peña MJ, McLean R, Suits MD, Boraston AB, Atherly T, Ziemer CJ, Williams SJ, Davies GJ, Abbott DW, Martens EC, and Gilbert HJ. (2015). Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism. Nature. 2015;517(7533):165-169. DOI:10.1038/nature13995 |