8JKV

membrane proteins


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and mechanism of lysosome transmembrane acetylation by HGSNAT.

Xu, R.Ning, Y.Ren, F.Gu, C.Zhu, Z.Pan, X.Pshezhetsky, A.V.Ge, J.Yu, J.

(2024) Nat Struct Mol Biol 31: 1502-1508

  • DOI: https://doi.org/10.1038/s41594-024-01315-5
  • Primary Citation of Related Structures:  
    8JKV, 8JL1, 8JL3, 8W4A

  • PubMed Abstract: 

    Lysosomal transmembrane acetylation of heparan sulfates (HS) is catalyzed by HS acetyl-CoA:α-glucosaminide N-acetyltransferase (HGSNAT), whose dysfunction leads to lysosomal storage diseases. The mechanism by which HGSNAT, the sole non-hydrolase enzyme in HS degradation, brings cytosolic acetyl-coenzyme A (Ac-CoA) and lysosomal HS together for N-acyltransferase reactions remains unclear. Here, we present cryogenic-electron microscopy structures of HGSNAT alone, complexed with Ac-CoA and with acetylated products. These structures explain that Ac-CoA binding from the cytosolic side causes dimeric HGSNAT to form a transmembrane tunnel. Within this tunnel, catalytic histidine and asparagine approach the lumen and instigate the transfer of the acetyl group from Ac-CoA to the glucosamine group of HS. Our study unveils a transmembrane acetylation mechanism that may help advance therapeutic strategies targeting lysosomal storage diseases.


  • Organizational Affiliation

    Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Heparan-alpha-glucosaminide N-acetyltransferase
A, B
706Homo sapiensMutation(s): 0 
Gene Names: HGSNATTMEM76
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: 3Go to GlyGen: Q68CP4-1
Sequence Annotations
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  • 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, D, E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
Query on CLR

Download Ideal Coordinates CCD File 
CB [auth B],
S [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
R16
Query on R16

Download Ideal Coordinates CCD File 
JA [auth A],
SB [auth B]
HEXADECANE
C16 H34
DCAYPVUWAIABOU-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
G [auth A],
QA [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
C14
Query on C14

Download Ideal Coordinates CCD File 
AB [auth B]
DA [auth A]
EA [auth A]
EB [auth B]
FA [auth A]
AB [auth B],
DA [auth A],
EA [auth A],
EB [auth B],
FA [auth A],
FB [auth B],
GA [auth A],
K [auth A],
L [auth A],
M [auth A],
MB [auth B],
N [auth A],
NB [auth B],
O [auth A],
OB [auth B],
PB [auth B],
Q [auth A],
U [auth A],
UA [auth B],
V [auth A],
VA [auth B],
WA [auth B],
XA [auth B],
YA [auth B]
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12
Query on D12

Download Ideal Coordinates CCD File 
H [auth A]
IB [auth B]
OA [auth A]
PA [auth B]
RA [auth B]
H [auth A],
IB [auth B],
OA [auth A],
PA [auth B],
RA [auth B],
Y [auth A]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10
Query on D10

Download Ideal Coordinates CCD File 
HB [auth B],
X [auth A]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT
Query on OCT

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AA [auth A]
BA [auth A]
BB [auth B]
CA [auth A]
DB [auth B]
AA [auth A],
BA [auth A],
BB [auth B],
CA [auth A],
DB [auth B],
GB [auth B],
HA [auth A],
I [auth A],
IA [auth A],
J [auth A],
JB [auth B],
KA [auth A],
KB [auth B],
LA [auth A],
LB [auth B],
MA [auth A],
NA [auth A],
P [auth A],
QB [auth B],
R [auth A],
RB [auth B],
SA [auth B],
T [auth A],
TA [auth B],
TB [auth B],
UB [auth B],
VB [auth B],
W [auth A],
Z [auth A],
ZA [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.87 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-10-30
    Changes: Data collection, Database references
  • Version 1.3: 2024-11-06
    Changes: Data collection