2RI8: Penicillium citrinum alpha-1,2-mannosidase complex with glycerol

Class I alpha-mannosidases (glycoside hydrolase family GH47) play key roles in the maturation of N-glycans and the ER-associated degradation of unfolded glycoproteins. The 1.95 A resolution structure of a fungal alpha-1,2-mannosidase in complex with the substrate analogue methyl-alpha-D-lyxopyranosyl-(1',2)-alpha-D-mannopyranoside (LM) shows the intact disaccharide spanning the -1/+1 subsites, with the D-lyxoside ring in the -1 subsite in the 1C4 chair conformation, and provides insight into the mechanism of catalysis. The absence of the C5' hydroxymethyl group on the D-lyxoside moiety results in the side chain of Arg407 adopting two alternative conformations: the minor one interacting with Asp375 and the major one interacting with both the D-lyxoside and the catalytic base Glu409, thus disrupting its function. Chemical modification of Asp375 has previously been shown to inactivate the enzyme. Taken together, the data suggest that Arg407, which belongs to the conserved sequence motif RPExxE, may act to modulate the activity of the enzyme. The proposed mechanism for modulating the activity is potentially a general mechanism for this superfamily.
PDB ID: 2RI8Download
MMDB ID: 63247
PDB Deposition Date: 2007/10/10
Updated in MMDB: 2012/11
Experimental Method:
x-ray diffraction
Resolution: 2.16  Å
Source Organism:
Similar Structures:
Biological Unit for 2RI8: monomeric; determined by author and by software (PISA)
Molecular Components in 2RI8
Label Count Molecule
Protein (1 molecule)
Mannosyl-oligosaccharide Alpha-1,2-mannosidase
Molecule annotation
Chemicals (11 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB