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Difference between revisions of "Carbohydrate Binding Module Family 94"
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== Structural Features == | == Structural Features == | ||
| − | + | CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and ''B. mori'' ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB 7XTL, 7VMT, and 7XTM), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while ''B. mori'' CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as GlcNAc-binding CBM32 domain of ''Clostridium perfringens'' GH84 β-''N''-acetylglucosaminidase NagH. The 1.15-Å resolution structure of ''B. mori'' CBM94 in complex with β-GlcNAc indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc. | |
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== Functionalities == | == Functionalities == | ||
Revision as of 01:08, 20 January 2023
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.
| CAZy DB link | |
| http://www.cazy.org/CBM94.html |
Ligand specificities
CBM94 was established in 2022 after the structural and functional characterization of the C-terminal domains of human N-acetylglucosaminyltransferase IVa (GnT-IVa, MGAT4A; GT54; EC 2.4.1.145) and an ortholog from lepidopteran insect Bombyx mori [1]. The CBM94 proteins from human and B. mori showed affinity toward N-acetylglucosamine, N,N’-diacetylchitobiose, and p-nitrophenyl β-N-acetylglucosaminide with Ka values of 242–1,970 M−1. No affinity was detected for other monosaccharides, including glucose, mannose, galactose, L-fucose, and N-acetylgalactosamine, some of which are components of matured N-glycans [1]. Nagae et al. demonstrated that the C-terminal domain of mouse GnT-IVa has binding ability for GlcNAc and GlcNAcβ1-2Man using NMR titration analysis [2]. Furthermore, comprehensive frontal affinity chromatography analysis using 157 glycans showed that mouse CBM94 has affinity for N-glycans with β-(1→2) and β-(1→4)-linked GlcNAc at the non-reducing ends. On the other hand, it showed low affinity for N-glycan with only β-(1→2)-linked GlcNAc, which is the substrate of GnT-IV [2]. Therefore, CBM94 prefers product N-glycans rather than substrate N-glycans.
Structural Features
CBM94 domains of GnT-IV enzymes comprise of around 150 amino acid residues. The crystal structures of the CBM94 domains in human and mouse GnT-IVa and B. mori ortholog were determined at 1.97, 1.95, and 1.47 Å resolution (PDB 7XTL, 7VMT, and 7XTM), respectively. The mammalian CBM94 adopt β-sandwich fold comprising nine β-strands and three short α-helices, while B. mori CBM94 has a similar fold but lacks one α-helix. They are structurally homologous to CBM32 proteins, such as GlcNAc-binding CBM32 domain of Clostridium perfringens GH84 β-N-acetylglucosaminidase NagH. The 1.15-Å resolution structure of B. mori CBM94 in complex with β-GlcNAc indicates that Tyr429, Trp445, Asp480, and Trp535 contribute to GlcNAc binding. These residues are completely conserved among CBM94 domains in mammalian GnT-IV isozymes (GnT-IVa, GnT-IVb, and GnT-IVc) except that Tyr429 is substituted to Phe in GnT-IVc.
Functionalities
Content in this section should include, in paragraph form, a description of:
- Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
- Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
- Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.
Family Firsts
- First Identified
- Sugar-binding ability of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and Bombyx mori ortholog was identified independently by two groups [1, 2].
- First Structural Characterization
- Crystal structures of the C-terminal domains of human and mouse GnT-IVa (MGAT4A) and Bombyx mori ortholog were determined independently by two groups [1, 2]. β-GlcNAc-bound structure of B. mori CBM94 was also determined [1].
References
- Oka N, Mori S, Ikegaya M, Park EY, and Miyazaki T. (2022). Crystal structure and sugar-binding ability of the C-terminal domain of N-acetylglucosaminyltransferase IV establish a new carbohydrate-binding module family. Glycobiology. 2022;32(12):1153-1163. DOI:10.1093/glycob/cwac058 |
- Nagae M, Hirata T, Tateno H, Mishra SK, Manabe N, Osada N, Tokoro Y, Yamaguchi Y, Doerksen RJ, Shimizu T, and Kizuka Y. (2022). Discovery of a lectin domain that regulates enzyme activity in mouse N-acetylglucosaminyltransferase-IVa (MGAT4A). Commun Biol. 2022;5(1):695. DOI:10.1038/s42003-022-03661-w |
- Osada N, Nagae M, Nakano M, Hirata T, and Kizuka Y. (2022). Examination of differential glycoprotein preferences of N-acetylglucosaminyltransferase-IV isozymes a and b. J Biol Chem. 2022;298(9):102400. DOI:10.1016/j.jbc.2022.102400 |