PDBsum entry 1kkt

Hydrolase

PDB id: 1kkt

Contents

Protein chains

475 a.a. *

Ligands

NAG-NAG ×4

NAG-NAG-MAN-MAN-MAN ×2

Metals

_CA ×2

Waters ×201

* Residue conservation analysis

PDB id:

1kkt

Name:

Hydrolase

Title:

Structure of p. Citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the er and golgi class i enzymes

Structure:

Mannosyl-oligosaccharide alpha-1,2-mannosidase. Chain: a, b. Synonym: man(9)-alpha-mannosidase. Engineered: yes

Source:

Penicillium citrinum. Organism_taxid: 5077. Gene: msdc. Expressed in: aspergillus oryzae. Expression_system_taxid: 5062.

Resolution:

2.20Å R-factor: 0.193 R-free: 0.239

Authors:

Y.D.Lobsanov,F.Vallee,A.Imberty,T.Yoshida,P.Yip,A.Herscovics, P.L.Howell

Key ref:

Y.D.Lobsanov et al. (2002). Structure of Penicillium citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the endoplasmic reticulum and Golgi class I enzymes. J Biol Chem, 277, 5620-5630. PubMed id: 11714724 DOI: 10.1074/jbc.M110243200

Date:

10-Dec-01 Release date: 23-Jan-02

Protein chains

P31723  (MAN12_PENCI) -  Mannosyl-oligosaccharide alpha-1,2-mannosidase from Penicillium citrinum

Seq: 511 a.a.

Struc: 475 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.1.113 - mannosyl-oligosaccharide 1,2-alpha-mannosidase.
• Reaction:
  1. N₄-(alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)- [alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man- (1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta- D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 9A1,2,3B1,2,3) + 4 H2O = N₄-(alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man- (1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta- D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 5A1,2) + 4 beta-D-mannose
  2. N₄-(alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)- [alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man- (1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L- asparaginyl-[protein] (N-glucan mannose isomer 8A1,2,3B1,3) + 3 H2O = N₄-(alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-alpha- D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L- asparaginyl-[protein] (N-glucan mannose isomer 5A1,2) + 3 beta-D-mannose.CC -!- This family of mammalian enzymes, located in the Golgi system,

N(4)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)- [alpha-D-Man-(1->2)-alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man- (1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta- D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 9A1,2,3B1,2,3) + 4 × H2O = N(4)-(alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man- (1->6)]-alpha-D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta- D-GlcNAc)-L-asparaginyl-[protein] (N-glucan mannose isomer 5A1,2) (Bound ligand (Het Group name = MAN) matches with 91.67% similarity) + 4 × beta-D-mannose

N(4)-(alpha-D-Man-(1->2)-alpha-D-Man-(1->2)-alpha-D-Man-(1->3)- [alpha-D-Man-(1->3)-[alpha-D-Man-(1->2)-alpha-D-Man-(1->6)]-alpha-D-Man- (1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L- asparaginyl-[protein] (N-glucan mannose isomer 8A1,2,3B1,3) + 3 × H2O = N(4)-(alpha-D-Man-(1->3)-[alpha-D-Man-(1->3)-[alpha-D-Man-(1->6)]-alpha- D-Man-(1->6)]-beta-D-Man-(1->4)-beta-D-GlcNAc-(1->4)-beta-D-GlcNAc)-L- asparaginyl-[protein] (N-glucan mannose isomer 5A1,2) (Bound ligand (Het Group name = MAN) matches with 91.67% similarity) + 3 × beta-D-mannose.CC -!- This family of mammalian enzymes, located in the Golgi system,

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.M110243200

J Biol Chem 277:5620-5630 (2002)

PubMed id: 11714724

Structure of Penicillium citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the endoplasmic reticulum and Golgi class I enzymes.

Y.D.Lobsanov, F.Vallée, A.Imberty, T.Yoshida, P.Yip, A.Herscovics, P.L.Howell.

ABSTRACT

Class I alpha1,2-mannosidases (glycosylhydrolase family 47) are key enzymes in the maturation of N-glycans. This protein family includes two distinct enzymatically active subgroups. Subgroup 1 includes the yeast and human endoplasmic reticulum (ER) alpha1,2-mannosidases that primarily trim Man(9)GlcNAc(2) to Man(8)GlcNAc(2) isomer B whereas subgroup 2 includes mammalian Golgi alpha1,2-mannosidases IA, IB, and IC that trim Man(9)GlcNAc(2) to Man(5)GlcNAc(2) via Man(8)GlcNAc(2) isomers A and C. The structure of the catalytic domain of the subgroup 2 alpha1,2-mannosidase from Penicillium citrinum has been determined by molecular replacement at 2.2-A resolution. The fungal alpha1,2-mannosidase is an (alphaalpha)(7)-helix barrel, very similar to the subgroup 1 yeast (Vallée, F., Lipari, F., Yip, P., Sleno, B., Herscovics, A., and Howell, P. L. (2000) EMBO J. 19, 581-588) and human (Vallée, F., Karaveg, K., Herscovics, A., Moremen, K. W., and Howell, P. L. (2000) J. Biol. Chem. 275, 41287-41298) ER enzymes. The location of the conserved acidic residues of the catalytic site and the binding of the inhibitors, kifunensine and 1-deoxymannojirimycin, to the essential calcium ion are conserved in the fungal enzyme. However, there are major structural differences in the oligosaccharide binding site between the two alpha1,2-mannosidase subgroups. In the subgroup 1 enzymes, an arginine residue plays a critical role in stabilizing the oligosaccharide substrate. In the fungal alpha1,2-mannosidase this arginine is replaced by glycine. This replacement and other sequence variations result in a more spacious carbohydrate binding site. Modeling studies of interactions between the yeast, human and fungal enzymes with different Man(8)GlcNAc(2) isomers indicate that there is a greater degree of freedom to bind the oligosaccharide in the active site of the fungal enzyme than in the yeast and human ER alpha1,2-mannosidases.

Selected figure(s)

Figure 1.
Fig. 1. Schematic representation of the Man[9]GlcNAc[2]. The mannose residues are labeled M3 to M11. Removal of mannose residues M11, M10, and M9 results in the formation of Man[8]GlcNAc[2] isomers A, B, and C, respectively. Residues on each of the A, B, and C branches are colored purple, red, and orange, respectively. The torsion angles varied in the energy calculations, and the corresponding glycosidic linkages are labeled according to the type of saccharide unit (M, mannose; GN, N-acetylglucosamine), the chemical linkage (12, 1,2; 13, 1,3; 14, 1,4; 16, 1,6), and the branch they belong to (A, B, C). To distinguish the 1,2 linkages between M11 and M8 from that between M8 and M5 on branch A, the linkage between M11 and M8 is designated M12M-AA.

Figure 4.
Fig. 4. A, structural superposition of the conserved acidic residues and calcium ions in the active site region of the fungal (red), yeast (yellow), and human (blue) enzymes. Only a subset of the 11 catalytic residues is shown for clarity. Superposition was done with LSQMAN (34) using all C[ ]atoms. B, structural superposition of the FM·dMNJ ( pink), FM·KIF (purple), HM·dMNJ (yellow), and HM·KIF (green). Only residues implicated in catalysis are shown. The following fungal residues are shown (the equivalent yeast numbering is in parentheses): Glu122 (Glu132), Asp267 (Asp275), Ser268 (Ser276), Glu271 (Glu279), Glu409 (Glu435), Glu412 (Glu438), Glu472 (Glu503), Thr501 (Thr525), Glu502 (Glu526).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 5620-5630) copyright 2002.

Figures were selected by an automated process.