Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 55.98 kDa 
• Atom Count: 4110 
• Modelled Residue Count: 467 
• Deposited Residue Count: 478 
• Unique protein chains: 1

1NXC

Structure of mouse Golgi alpha-1,2-mannosidase IA reveals the molecular basis for substrate specificity among Class I enzymes (family 47 glycosidases)

• PDB DOI: 10.2210/pdb1NXC/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2003-02-10 Released: 2004-05-04 
• Deposition Author(s): Tempel, W., Liu, Z.-J., Karaveg, K., Rose, J., Moremen, K.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.190 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 

Literature

Structure of mouse Golgi alpha-mannosidase IA reveals the molecular basis for substrate specificity among class 1 (family 47 glycosylhydrolase) alpha1,2-mannosidases

Tempel, W., Karaveg, K., Liu, Z.-J., Rose, J., Wang, B.-C., Moremen, K.W.

(2004) J Biol Chem 279: 29774-29786

• PubMed: 15102839 
• DOI: 10.1074/jbc.M403065200
• Primary Citation of Related Structures:  
  1NXC


• PubMed Abstract: 
  

Three subfamilies of mammalian Class 1 processing alpha1,2-mannosidases (family 47 glycosidases) play critical roles in the maturation of Asn-linked glycoproteins in the endoplasmic reticulum (ER) and Golgi complex as well as influencing the timing and recognition for disposal of terminally unfolded proteins by ER-associated degradation. In an effort to define the structural basis for substrate recognition among Class 1 mannosidases, we have crystallized murine Golgi mannosidase IA (space group P2(1)2(1)2(1)), and the structure was solved to 1.5-A resolution by molecular replacement. The enzyme assumes an (alphaalpha)(7) barrel structure with a Ca(2+) ion coordinated at the base of the barrel similar to other Class 1 mannosidases. Critical residues within the barrel structure that coordinate the Ca(2+) ion or presumably bind and catalyze the hydrolysis of the glycone are also highly conserved. A Man(6)GlcNAc(2) oligosaccharide attached to Asn(515) in the murine enzyme was found to extend into the active site of an adjoining protein unit in the crystal lattice in a presumed enzyme-product complex. In contrast to an analogous complex previously isolated for Saccharomyces cerevisiae ER mannosidase I, the oligosaccharide in the active site of the murine Golgi enzyme assumes a different conformation to present an alternate oligosaccharide branch into the active site pocket. A comparison of the observed protein-carbohydrate interactions for the murine Golgi enzyme with the binding cleft topologies of the other family 47 glycosidases provides a framework for understanding the structural basis for substrate recognition among this class of enzymes.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA	A	478	Mus musculus	Mutation(s): 0  Gene Names: Man1a, Man1a1 EC: 3.2.1.113
UniProt
Find proteins for P45700 (Mus musculus) Explore P45700  Go to UniProtKB:  P45700

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G92684AL GlyCosmos:  G92684AL GlyGen:  G92684AL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.51 Å
• R-Value Free: 0.190 
• R-Value Work: 0.171 
• R-Value Observed: 0.172 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.288	α = 90
b = 72.164	β = 90
c = 129.571	γ = 90

Software Package:

Software Name	Purpose
EPMR	phasing
REFMAC	refinement
PROTEUM PLUS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-02-10 
• Released Date: 2004-05-04 
Deposition Author(s): Tempel, W., Liu, Z.-J., Karaveg, K., Rose, J., Moremen, K.W., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG)

Revision History  

• Version 1.0: 2004-05-04
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary