PDBsum entry: 1fmi

Hydrolase

PDB id: 1fmi

Contents

Protein chain

456 a.a. *

Ligands

SO4 ×3

Metals

_CA

Waters ×391

* Residue conservation analysis

PDB id:

1fmi

Name:

Hydrolase

Title:

Crystal structure of human class i alpha1,2-mannosidase

Structure:

Endoplasmic reticulum alpha-mannosidase i. Chain: a. Synonym: class i alpha1,2-mannosidase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932.

Resolution:

1.90Å R-factor: 0.222 R-free: 0.250

Authors:

F.Vallee,K.Karaveg,A.Herscovics,K.W.Moremen,P.L.Howell

Key ref:

F.Vallee et al. (2000). Structural basis for catalysis and inhibition of N-glycan processing class I alpha 1,2-mannosidases. J Biol Chem, 275, 41287-41298. PubMed id: 10995765 DOI: 10.1074/jbc.M006927200

Date:

17-Aug-00 Release date: 17-Jan-01

Protein chain

Q9UKM7  (MA1B1_HUMAN) -  Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase

Seq: 699 a.a.

Struc: 456 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.2.1.113 - Mannosyl-oligosaccharide 1,2-alpha-mannosidase.
• Reaction: Hydrolysis of the terminal 1,2-linked alpha-D-mannose residues in the oligo-mannose oligosaccharide Man(9)(GlcNAc)(2).

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)
• Biochemical function: calcium ion binding (2 terms)

DOI no: 10.1074/jbc.M006927200

J Biol Chem 275:41287-41298 (2000)

PubMed id: 10995765

Structural basis for catalysis and inhibition of N-glycan processing class I alpha 1,2-mannosidases.

F.Vallee, K.Karaveg, A.Herscovics, K.W.Moremen, P.L.Howell.

ABSTRACT

Endoplasmic reticulum (ER) class I alpha1,2-mannosidase (also known as ER alpha-mannosidase I) is a critical enzyme in the maturation of N-linked oligosaccharides and ER-associated degradation. Trimming of a single mannose residue acts as a signal to target misfolded glycoproteins for degradation by the proteasome. Crystal structures of the catalytic domain of human ER class I alpha1,2-mannosidase have been determined both in the presence and absence of the potent inhibitors kifunensine and 1-deoxymannojirimycin. Both inhibitors bind to the protein at the bottom of the active-site cavity, with the essential calcium ion coordinating the O-2' and O-3' hydroxyls and stabilizing the six-membered rings of both inhibitors in a (1)C(4) conformation. This is the first direct evidence of the role of the calcium ion. The lack of major conformational changes upon inhibitor binding and structural comparisons with the yeast alpha1, 2-mannosidase enzyme-product complex suggest that this class of inverting enzymes has a novel catalytic mechanism. The structures also provide insight into the specificity of this class of enzymes and provide a blueprint for the future design of novel inhibitors that prevent degradation of misfolded proteins in genetic diseases.

Selected figure(s)

Figure 3.
Fig. 3. Binding of 1-deoxymannojirimycin and kifunensine to human ER class I 1,2-mannosidase. A, location of kifunensine in the center of the ( )[7]-barrel. 1-Deoxymannojirimycin superimposes with the six-membered ring of kifunensine, but for clarity, it is not represented in this panel. The color scheme is the same as described in the legend to Fig. 2. B and C, schematic representation of the interactions between human 1,2-mannosidase and kifunensine and 1-deoxymannojirimycin, respectively. Short and long dashed lines represent hydrogen bond interactions and van der Waals contacts, respectively. For simplicity, only hydrogen bonds between the protein, water, and inhibitor molecules are represented. Water-water hydrogen bonds are not represented. D, surface representation of the catalytic cavity of human 1,2-mannosidase in the vicinity of the kifunensine-binding site. The surface is colored according to its electrostatic potential. Kifunensine is shown in stick representation. The contour level is at ±20 kT. A was prepared using MOLSCRIPT (70), and D was prepared with GRASP (72).

Figure 5.
Fig. 5. Catalytic mechanism. A, schematic representation of the high-mannose Man[9]GlcNAc oligosaccharide showing the 1,2-linkage that is cleaved and numbering of the saccharide units. B, structural superimposition of the active-site region of HM·dMNJ, HM·KIF , and yeast class I 1,2-mannosidases. The Man7 (M7) residue of the middle-arm branch of the N-glycan, the amino acid residues, and the glycerol molecule of yeast 1,2-mannosidases are yellow. The HM·KIF and HM·dMNJ structures are blue and green, respectively. Calcium, whose position is invariant in the three structures, is shown in dark blue. C, close-up of the putative linkage between the O-2' atom of Man7 in yeast 1,2-mannosidases and the C-1 atom of 1-deoxymannojirimycin in the HM·dMNJ structure. The atom colored red lies in the plane defined by the nitrogen, C-2, C-3, and C-5 atoms and represents the putative deformation of the ring during catalysis. D, proposed catalytic mechanism as described under "Results and Discussion." W, water.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 41287-41298) copyright 2000.

Figures were selected by an automated process.