Glycoside Hydrolase Family 38

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• Author: David Rose
• Responsible Curator: David Rose

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Glycoside Hydrolase Family GH38
Clan	none
Mechanism	retaining
Active site residues	known
CAZy DB link
https://www.cazy.org/GH38.html

Substrate specificities

Glycoside hydrolases of family 38 are Class II α-mannosidases. They range in breadth of specificity from the Golgi α-mannosidase (2A1), which has a dual specificity for α-1,6 and α-1,3-linked mannoses, to the lysosomal mannosidases, which have either broad (2B1 cleaves α1,2, α1,3 and α1,6 linkages) or narrow specificities (2B2 is specific for α-1,6). GH38 active sites can be quite long and open, and some are sensitive to the polysaccharide substrate structure. For example, Golgi α-mannosidase II requires the presence of a GlcNAc residue some five residues away from the cleavage site, while lysosomal mannosidases do not have that requirement [1, 2]. There have been GH38 mannosidases identified in a number of different localizations, classed into subfamilies with different substrate specificities and biochemical properties, and, presumably, different physiological roles. The Golgi enzyme is identified as 2A1 (Class 2, A for Golgi, enzyme 1). Lysosomal GH38 mannosidases are indicated by 'B' (2B1, 2B2) and those likely existing in the cytoplasm by 'C'. Physiological roles have been identified for the Golgi enzyme in the protein N-glycosylation pathway and lysosomal mannosidases in general are likely to be involved in scavenging of degraded glycoproteins. Roles for the cytoplasmic subclass have not been identified definitively, but they may play a role in protein recognition or signalling.

Kinetics and Mechanism

GH38 enzymes are anomeric-configuration retaining enzymes that operate by the classical Koshland double-displacement mechanism. This was initially determined by trapping of the covalent intermediate with jack bean α-mannosidase [3] and later confirmed by structural analysis of covalent intermediates [4]

Catalytic Residues

Both catalytic side chains are Asp residues. The catalytic nucleophile of Asp204 (Golgi α-mannosidase II crystal structure numbering) was inferred from previous studies with jack Bean α-mannosidase [3] and confirmed in the crystal structures of covalent intermediates [4]. Mutagenesis studies implicated Asp341 as the likely catalytic acid/base residue.

Three-dimensional structures

The crystal structure of the GH38 domain of Drosophila Golgi α-mannosidase II [1] has been determined in complex with a large number of inhibitors and intermediate mimics. Many of these are at very high resolution: 1.2-1.6Å (see [5, 6, 7, 8, 9] for examples). An enzyme-substrate complex has also been determined [10]. The crystal structure of bovine lysosomal α-mannosidase II was determined to 2.7Å resolution and displayedinteresting low-pH activation effects [11]. Some of the lysosomal enzymes show a metal dependency for activity. Mutations in the residues proposed to be involved with metal binding are associated with lysosomal storage diseases [12]. The GH38 fold has been referred to as the "mannosidase fold". It is one large (approximately 1000-residue) globular domain, which can be roughly divided by secondary structure into an α/β portion and an all-β region. The former portion contains the active site, anchored by a Zn atom, which forms an integral part of the -1 site, interacting with the saccharide and helping to induce substrate distortion [1].

Family Firsts

First sterochemistry determination

First catalytic nucleophile identification

Jack bean mannosidase [3]

First general acid/base residue identification

Golgi α-mannosidase II covalent intermediate stabilization [4]

First 3-D structure

Golgi α-mannosidase II [1]

References

1. van den Elsen JM, Kuntz DA, and Rose DR. (2001). Structure of Golgi alpha-mannosidase II: a target for inhibition of growth and metastasis of cancer cells. EMBO J. 2001;20(12):3008-17. DOI:10.1093/emboj/20.12.3008 |
2. Park C, Meng L, Stanton LH, Collins RE, Mast SW, Yi X, Strachan H, and Moremen KW. (2005). Characterization of a human core-specific lysosomal {alpha}1,6-mannosidase involved in N-glycan catabolism. J Biol Chem. 2005;280(44):37204-16. DOI:10.1074/jbc.M508930200 |
3. Howard S, He S, and Withers SG. (1998). Identification of the active site nucleophile in jack bean alpha-mannosidase using 5-fluoro-beta-L-gulosyl fluoride. J Biol Chem. 1998;273(4):2067-72. DOI:10.1074/jbc.273.4.2067 |
4. Numao S, Kuntz DA, Withers SG, and Rose DR. (2003). Insights into the mechanism of Drosophila melanogaster Golgi alpha-mannosidase II through the structural analysis of covalent reaction intermediates. J Biol Chem. 2003;278(48):48074-83. DOI:10.1074/jbc.M309249200 |
5. Shah N, Kuntz DA, and Rose DR. (2003). Comparison of kifunensine and 1-deoxymannojirimycin binding to class I and II alpha-mannosidases demonstrates different saccharide distortions in inverting and retaining catalytic mechanisms. Biochemistry. 2003;42(47):13812-6. DOI:10.1021/bi034742r |
6. Kawatkar SP, Kuntz DA, Woods RJ, Rose DR, and Boons GJ. (2006). Structural basis of the inhibition of Golgi alpha-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions. J Am Chem Soc. 2006;128(25):8310-9. DOI:10.1021/ja061216p |
7. Kumar NS, Kuntz DA, Wen X, Pinto BM, and Rose DR. (2008). Binding of sulfonium-ion analogues of di-epi-swainsonine and 8-epi-lentiginosine to Drosophila Golgi alpha-mannosidase II: the role of water in inhibitor binding. Proteins. 2008;71(3):1484-96. DOI:10.1002/prot.21850 |
8. Zhong W, Kuntz DA, Ember B, Singh H, Moremen KW, Rose DR, and Boons GJ. (2008). Probing the substrate specificity of Golgi alpha-mannosidase II by use of synthetic oligosaccharides and a catalytic nucleophile mutant. J Am Chem Soc. 2008;130(28):8975-83. DOI:10.1021/ja711248y |
9. Fiaux H, Kuntz DA, Hoffman D, Janzer RC, Gerber-Lemaire S, Rose DR, and Juillerat-Jeanneret L. (2008). Functionalized pyrrolidine inhibitors of human type II alpha-mannosidases as anti-cancer agents: optimizing the fit to the active site. Bioorg Med Chem. 2008;16(15):7337-46. DOI:10.1016/j.bmc.2008.06.021 |
10. Shah N, Kuntz DA, and Rose DR. (2008). Golgi alpha-mannosidase II cleaves two sugars sequentially in the same catalytic site. Proc Natl Acad Sci U S A. 2008;105(28):9570-5. DOI:10.1073/pnas.0802206105 |
11. Heikinheimo P, Helland R, Leiros HK, Leiros I, Karlsen S, Evjen G, Ravelli R, Schoehn G, Ruigrok R, Tollersrud OK, McSweeney S, and Hough E. (2003). The structure of bovine lysosomal alpha-mannosidase suggests a novel mechanism for low-pH activation. J Mol Biol. 2003;327(3):631-44. DOI:10.1016/s0022-2836(03)00172-4 |
12. Venkatesan M, Kuntz DA, and Rose DR. (2009). Human lysosomal alpha-mannosidases exhibit different inhibition and metal binding properties. Protein Sci. 2009;18(11):2242-51. DOI:10.1002/pro.235 |