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Fungal α‐mannosidase Ams1 and its mammalian homolog MAN2C1 hydrolyze terminal α‐linked mannoses in free oligosaccharides released from misfolded glycoproteins or lipid‐linked oligosaccharide donors. Ams1 is transported by selective autophagy into vacuoles. Here, we determine the tetrameric structure of Ams1 from the fission yeast Schizosaccharomyces pombe at 3.2 Å resolution by cryo‐electron microscopy. Distinct from a low resolution structure of S. cerevisiae Ams1, S. pombe Ams1 has a prominent N‐terminal tail that mediates tetramerization and an extra β‐sheet domain. Ams1 shares a conserved active site with other enzymes in glycoside hydrolase family 38, to which Ams1 belongs, but contains extra N‐terminal domains involved in tetramerization. The atomic structure of Ams1 reported here will aid understanding of its enzymatic activity and transport mechanism.