5KIJ

Crystal structure of the class I human endoplasmic reticulum 1,2-alpha-mannosidase and Man9GlcNAc2-PA complex

Summary for 5KIJ

• Entry DOI: 10.2210/pdb5kij/pdb
• Descriptor: Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, LANTHANUM (III) ION, ... (7 entities in total)
• Functional Keywords: alpha/alpha-barrel, cation replacement, protein-glycan interaction, hydrolase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 54441.18

Authors

Karaveg, K.,Xiang, Y.,Moremen, K.W. (deposition date: 2016-06-16, release date: 2017-05-10, Last modification date: 2024-11-06)

Primary citation

Xiang, Y.,Karaveg, K.,Moremen, K.W.
Substrate recognition and catalysis by GH47 alpha-mannosidases involved in Asn-linked glycan maturation in the mammalian secretory pathway.
Proc. Natl. Acad. Sci. U.S.A., 113:E7890-E7899, 2016

PubMed Abstract: Maturation of Asn-linked oligosaccharides in the eukaryotic secretory pathway requires the trimming of nascent glycan chains to remove all glucose and several mannose residues before extension into complex-type structures on the cell surface and secreted glycoproteins. Multiple glycoside hydrolase family 47 (GH47) α-mannosidases, including endoplasmic reticulum (ER) α-mannosidase I (ERManI) and Golgi α-mannosidase IA (GMIA), are responsible for cleavage of terminal α1,2-linked mannose residues to produce uniquely trimmed oligomannose isomers that are necessary for ER glycoprotein quality control and glycan maturation. ERManI and GMIA have similar catalytic domain structures, but each enzyme cleaves distinct residues from tribranched oligomannose glycan substrates. The structural basis for branch-specific cleavage by ERManI and GMIA was explored by replacing an essential enzyme-bound Ca ion with a lanthanum (La) ion. This ion swap led to enzyme inactivation while retaining high-affinity substrate interactions. Cocrystallization of La-bound enzymes with ManGlcNAc substrate analogs revealed enzyme-substrate complexes with distinct modes of glycan branch insertion into the respective enzyme active-site clefts. Both enzymes had glycan interactions that extended across the entire glycan structure, but each enzyme engaged a different glycan branch and used different sets of glycan interactions. Additional mutagenesis and time-course studies of glycan cleavage probed the structural basis of enzyme specificity. The results provide insights into the enzyme catalytic mechanisms and reveal structural snapshots of the sequential glycan cleavage events. The data also indicate that full steric access to glycan substrates determines the efficiency of mannose-trimming reactions that control the conversion to complex-type structures in mammalian cells.

PubMed: 27856750
DOI: 10.1073/pnas.1611213113

Experimental method

X-RAY DIFFRACTION (1.649 Å)