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TitleStructural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 1326, Year 2024
Publish dateFeb 13, 2024
AuthorsCourtney J Mycroft-West / Sahar Abdelkarim / Helen M E Duyvesteyn / Neha S Gandhi / Mark A Skidmore / Raymond J Owens / Liang Wu /
PubMed AbstractHeparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, ...Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo.
External linksNat Commun / PubMed:38351061 / PubMed Central
MethodsEM (single particle)
Resolution2.42 - 3.24 Å
Structure data

16564

8ccy

EMDB-16564, PDB-8ccy:
Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium and 3'-phosphoadenosine-5'-phosphosulfate
Method: EM (single particle) / Resolution: 2.7 Å

16565

8cd0

EMDB-16565, PDB-8cd0:
Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb7 (composite map and model)
Method: EM (single particle) / Resolution: 2.42 Å

EMDB-16626: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb7 (original map)
Method: EM (single particle) / Resolution: 2.63 Å

EMDB-16627: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb7 (locally refined map of N-terminal and deacetylase domains)
Method: EM (single particle) / Resolution: 2.42 Å

EMDB-16629: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb7 (locally refined map of deacetylase and sulfotransferase domains)
Method: EM (single particle) / Resolution: 2.42 Å

EMDB-16661: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb13 (original map)
Method: EM (single particle) / Resolution: 3.24 Å

EMDB-16662: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb13 (locally refined map of N-terminal and deacetylase domains)
Method: EM (single particle) / Resolution: 3.15 Å

EMDB-16663: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb13 (locally refined map of deacetylase and sulfotransferase domains)
Method: EM (single particle) / Resolution: 3.09 Å

16664

8chs

EMDB-16664, PDB-8chs:
Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate and nanobody nAb13 (composite map and model).
Method: EM (single particle) / Resolution: 3.15 Å

Chemicals

ChemComp-A3P:
ADENOSINE-3'-5'-DIPHOSPHATE / Adenosine 3',5'-bisphosphate

ChemComp-CA:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
  • lama glama (llama)
KeywordsCARBOHYDRATE / Deacetylase / Sulfotransferase / Heparan Sulfate / Glycosaminoglycan / Nanobody

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