Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 61092.16 
• Atom Count: 4260 
• Residue Count: 511 
• Unique protein chains: 1

1DL2

CRYSTAL STRUCTURE OF CLASS I ALPHA-1,2-MANNOSIDASE FROM SACCHAROMYCES CEREVISIAE AT 1.54 ANGSTROM RESOLUTION

• DOI: 10.2210/pdb1DL2/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Komagataella pastoris


• Deposited: 1999-12-08 Released: 2000-02-18 
• Deposition Author(s): Vallee, F., Lipari, F., Yip, P., Herscovics, A., Howell, P.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.227 
• R-Value Work: 0.209 

Literature

Crystal structure of a class I alpha1,2-mannosidase involved in N-glycan processing and endoplasmic reticulum quality control.

Vallee, F., Lipari, F., Yip, P., Sleno, B., Herscovics, A., Howell, P.L.

(2000) EMBO J. 19: 581-588

• PubMed: 10675327 
• DOI: 10.1093/emboj/19.4.581


• PubMed Abstract: 
  

Mannose trimming is not only essential for N-glycan maturation in mammalian cells but also triggers degradation of misfolded glycoproteins. The crystal structure of the class I alpha1, 2-mannosidase that trims Man(9)GlcNAc(2) to Man(8)GlcNAc(2 )isomer B in the endoplasmic reticulum of Saccharomyces cerevisiae reveals a novel (alphaalpha)(7)-barrel in which an N-glycan from one molecule extends into the barrel of an adjacent molecule, interacting with the essential acidic residues and calcium ion. The observed protein-carbohydrate interactions provide the first insight into the catalytic mechanism and specificity of this eukaryotic enzyme family and may be used to design inhibitors that prevent degradation of misfolded glycoproteins in genetic diseases.

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Organizational Affiliation: 

Structural Biology and Biochemistry, Research Institute, The Hospital for Sick Children, 555 University Avenue, Toronto, M5G 1X8, Ontario.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CLASS I ALPHA-1,2-MANNOSIDASE	A	511	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: MNS1 EC: 3.2.1.113
Find proteins for P32906 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: MNS1 Go to UniProtKB:  P32906

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MAN	A	ALPHA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
BMA	A	BETA-D-MANNOSE C6 H12 O6 WQZGKKKJIJFFOK-RWOPYEJCSA-N
NDG	A	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N
NAG	A	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.227 
• R-Value Work: 0.209 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 88.397	α = 90.00
b = 88.397	β = 90.00
c = 153.220	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNS	phasing
SCALEPACK	data scaling
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-12-08 
• Released Date: 2000-02-18 
• Deposition Author(s): Vallee, F., Lipari, F., Yip, P., Herscovics, A., Howell, P.L.

Revision History 

• Version 1.0: 2000-02-18
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-08-16
  Type: Advisory, Refinement description, Source and taxonomy