1DL2 | pdb_00001dl2

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

• PDB DOI: https://doi.org/10.2210/pdb1DL2/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Komagataella pastoris
• Mutation(s): No 


• 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 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

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: https://doi.org/10.1093/emboj/19.4.581
• Primary Citation Related Structures: 
  1DL2


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.95 kDa 
• Atom Count: 4,653 
• Modeled Residue Count: 510 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N/A
Glycosylation Resources
GlyTouCan: G34725OX GlyCosmos: G34725OX GlyGen: G34725OX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N/A
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.397	α = 90
b = 88.397	β = 90
c = 153.22	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-08-16
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-11-13
  Changes: Data collection, Database references, Structure summary