1KTC

The Structure of alpha-N-Acetylgalactosaminidase

• PDB DOI: https://doi.org/10.2210/pdb1KTC/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2002-01-15 Released: 2002-03-15 
• Deposition Author(s): Garman, S.C., Hannick, L., Zhu, A., Garboczi, D.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.231 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.

Garman, S.C., Hannick, L., Zhu, A., Garboczi, D.N.

(2002) Structure 10: 425-434

• PubMed: 12005440 
• DOI: https://doi.org/10.1016/s0969-2126(02)00726-8
• Primary Citation of Related Structures:  
  1KTB, 1KTC


• PubMed Abstract: 
  

  In the lysosome, glycosidases degrade glycolipids, glycoproteins, and oligosaccharides. Mutations in glycosidases cause disorders characterized by the deposition of undegraded carbohydrates. Schindler and Fabry diseases are caused by the incomplete degradation of carbohydrates with terminal alpha-N-acetylgalactosamine and alpha-galactose, respectively. Here we present the X-ray structure of alpha-N-acetylgalactosaminidase (alpha-NAGAL), the glycosidase that removes alpha-N-acetylgalactosamine, and the structure with bound ligand. The active site residues of alpha-NAGAL are conserved in the closely related enzyme a-galactosidase A (alpha-GAL). The structure demonstrates the catalytic mechanisms of both enzymes and reveals the structural basis of mutations causing Schindler and Fabry diseases. As alpha-NAGAL and alpha-GAL produce type O "universal donor" blood from type A and type B blood, the alpha-NAGAL structure will aid in the engineering of improved enzymes for blood conversion.

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Organizational Affiliation: 

Structural Biology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.19 kDa 
• Atom Count: 3,544 
• Modelled Residue Count: 388 
• Deposited Residue Count: 405 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
alpha-N-acetylgalactosaminidase	A	405	Gallus gallus	Mutation(s): 0  Gene Names: alpha-NAGA EC: 3.2.1.49
UniProt
Find proteins for Q90744 (Gallus gallus) Explore Q90744  Go to UniProtKB:  Q90744
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NGA	E [auth A]	2-acetamido-2-deoxy-beta-D-galactopyranose C8 H15 N O6 OVRNDRQMDRJTHS-JAJWTYFOSA-N
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY	U [auth A], V [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.231 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.93	α = 90
b = 72.93	β = 90
c = 176.413	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-15 
Deposition Author(s): Garman, S.C., Hannick, L., Zhu, A., Garboczi, D.N.

Revision History  

• Version 1.0: 2002-03-15
  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: 2011-11-16
  Changes: Atomic model
• 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: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary