CAZypedia needs your help! We have many unassigned GH, PL, CE, AA, GT, and CBM pages in need of Authors and Responsible Curators.
Scientists at all career stages, including students, are welcome to contribute to CAZypedia. Read more here, and in the 10th anniversary article in Glycobiology.
New to the CAZy classification? Read this first.
*
Consider attending the 15th Carbohydrate Bioengineering Meeting in Ghent, 5-8 May 2024.
Syn/anti lateral protonation
This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.
- Author: ^^^Wim Nerinckx^^^
- Responsible Curator: ^^^Spencer Williams^^^
Overview
This page will provide a table (and eventually a full lexicon article) on the spatial positioning of the catalytic general acid residue in the active sites of glycoside hydrolases. The table below updates those found in the seminal paper on this concept by Heightman and Vasella [1], and the more recent summary by Nerinckx et al. [2].
Table
This table can be re-sorted by clicking on the icons in the header (javascript must be turned on in your browser). To reset the page to be sorted by GH family, click the page above the page title.
| Family | Clan | Anomeric specificity | Mechanism | General acid | syn/anti | Nucleophile or General base | Ligand | Organism | Enzyme | PDB ID | Primary reference |
|---|---|---|---|---|---|---|---|---|---|---|---|
| GH1 | A | beta | retaining | Glu160 | anti | Glu375 | product | Lactococcus lactis | 6-phosopho-beta-galactosidase | 4pbg | [3] |
| GH2 | A | beta | retaining | Glu461 | anti | Glu537 | GalF-glycenz. | Escherechia coli | beta-galactosidase | 1jz0 | [4] |
| GH9 | beta | inverting | Glu424 | anti | Asp55,Asp58 | product | Thermomonospora fusca | cellulase | 3tf4,4tf4 | [5] |
References
-
Heightman, T.D. and Vasella, A.T. (1999) Recent Insights into Inhibition, Structure, and Mechanism of Configuration-Retaining Glycosidases. Angewandte Chemie-International Edition 38(6), 750-770. Article online.
- Nerinckx W, Desmet T, Piens K, and Claeyssens M. (2005). An elaboration on the syn-anti proton donor concept of glycoside hydrolases: electrostatic stabilisation of the transition state as a general strategy. FEBS Lett. 2005;579(2):302-12. DOI:10.1016/j.febslet.2004.12.021 |
- Wiesmann C, Hengstenberg W, and Schulz GE. (1997). Crystal structures and mechanism of 6-phospho-beta-galactosidase from Lactococcus lactis. J Mol Biol. 1997;269(5):851-60. DOI:10.1006/jmbi.1997.1084 |
- Juers DH, Heightman TD, Vasella A, McCarter JD, Mackenzie L, Withers SG, and Matthews BW. (2001). A structural view of the action of Escherichia coli (lacZ) beta-galactosidase. Biochemistry. 2001;40(49):14781-94. DOI:10.1021/bi011727i |
- Irwin D, Shin DH, Zhang S, Barr BK, Sakon J, Karplus PA, and Wilson DB. (1998). Roles of the catalytic domain and two cellulose binding domains of Thermomonospora fusca E4 in cellulose hydrolysis. J Bacteriol. 1998;180(7):1709-14. DOI:10.1128/JB.180.7.1709-1714.1998 |