8VLG

Cryo-EM structure of human HGSNAT bound with Acetyl-CoA and substrate analog


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heparan-alpha-glucosaminide N-acetyltransferase
A, B
663Homo sapiensMutation(s): 0 
Gene Names: HGSNATTMEM76
EC: 2.3.1.78
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: 3Go to GlyGen: Q68CP4-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ACO (Subject of Investigation/LOI)
Query on ACO

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
ACETYL COENZYME *A
C23 H38 N7 O17 P3 S
ZSLZBFCDCINBPY-ZSJPKINUSA-N
A1ACY (Subject of Investigation/LOI)
Query on A1ACY

Download Ideal Coordinates CCD File 
G [auth A],
K [auth B]
4-methyl-2-oxo-2H-1-benzopyran-7-yl 2-amino-2-deoxy-beta-D-glucopyranoside
C16 H19 N O7
XPBYRVZLJCNXMD-JPIRQXTESA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
H [auth B],
J [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.15 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: 2024-10-23
    Changes: Data collection