Skip to main content

 8VLU | pdb_00008vlu

Cryo-EM structure of human HGSNAT bound with CoA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8VLU

This is version 1.2 of the entry. See complete history. 

Literature

Structural and mechanistic insights into a lysosomal membrane enzyme HGSNAT involved in Sanfilippo syndrome.

Zhao, B., Cao, Z., Zheng, Y., Nguyen, P., Bowen, A., Edwards, R.H., Stroud, R.M., Zhou, Y., Van Lookeren Campagne, M., Li, F.

(2024) Nat Commun 15: 5388-5388

  • DOI: https://doi.org/10.1038/s41467-024-49614-1
  • Primary Citation Related Structures: 
    8VKJ, 8VLG, 8VLI, 8VLU, 8VLV, 8VLY

  • PubMed Abstract: 

    Heparan sulfate (HS) is degraded in lysosome by a series of glycosidases. Before the glycosidases can act, the terminal glucosamine of HS must be acetylated by the integral lysosomal membrane enzyme heparan-α-glucosaminide N-acetyltransferase (HGSNAT). Mutations of HGSNAT cause HS accumulation and consequently mucopolysaccharidosis IIIC, a devastating lysosomal storage disease characterized by progressive neurological deterioration and early death where no treatment is available. HGSNAT catalyzes a unique transmembrane acetylation reaction where the acetyl group of cytosolic acetyl-CoA is transported across the lysosomal membrane and attached to HS in one reaction. However, the reaction mechanism remains elusive. Here we report six cryo-EM structures of HGSNAT along the reaction pathway. These structures reveal a dimer arrangement and a unique structural fold, which enables the elucidation of the reaction mechanism. We find that a central pore within each monomer traverses the membrane and controls access of cytosolic acetyl-CoA to the active site at its luminal mouth where glucosamine binds. A histidine-aspartic acid catalytic dyad catalyzes the transfer reaction via a ternary complex mechanism. Furthermore, the structures allow the mapping of disease-causing variants and reveal their potential impact on the function, thus creating a framework to guide structure-based drug discovery efforts.


  • Organizational Affiliation: 
    • Amgen Research, Department of Structural biology, South San Francisco, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 149.81 kDa 
  • Atom Count: 8,596 
  • Modeled Residue Count: 1,096 
  • Deposited Residue Count: 1,326 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Heparan-alpha-glucosaminide N-acetyltransferaseA [auth B],
B [auth A]
663Homo sapiensMutation(s): 0 
Gene Names: HGSNAT, TMEM76
EC: 2.3.1.78
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q68CP4 (Homo sapiens)
Explore Q68CP4 
Go to UniProtKB:  Q68CP4
PHAROS:  Q68CP4
GTEx:  ENSG00000165102 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ68CP4
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q68CP4-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COA
(Subject of Investigation/LOI)

Query on COA



Download:Ideal Coordinates CCD File
D [auth B],
J [auth A]
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth B]
E [auth B]
F [auth B]
G [auth A]
H [auth A]
C [auth B],
E [auth B],
F [auth B],
G [auth A],
H [auth A],
I [auth A],
K [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesK99MH119591
Other privateUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-26
    Type: Initial release
  • Version 1.1: 2024-10-16
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-13
    Changes: Data collection