8CD0

Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium, 3'-phosphoadenosine-5'-phosphosulfate, and nanobody nAb7 (composite map and model)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1.

Mycroft-West, C.J.Abdelkarim, S.Duyvesteyn, H.M.E.Gandhi, N.S.Skidmore, M.A.Owens, R.J.Wu, L.

(2024) Nat Commun 15: 1326-1326

  • DOI: https://doi.org/10.1038/s41467-024-45419-4
  • Primary Citation of Related Structures:  
    8CCY, 8CD0, 8CHS

  • PubMed Abstract: 

    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.


  • Organizational Affiliation

    The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1882Homo sapiensMutation(s): 0 
Gene Names: NDST1HSSTHSST1
EC: 3.5.1 (PDB Primary Data), 2.8.2.8 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P52848 (Homo sapiens)
Explore P52848 
Go to UniProtKB:  P52848
PHAROS:  P52848
GTEx:  ENSG00000070614 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP52848
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Nanobody nAb7B [auth C]162Lama glamaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--
Wellcome TrustUnited Kingdom060208/Z/00/Z
Wellcome TrustUnited Kingdom093305/Z/10/Z
Wellcome TrustUnited Kingdom203141/Z/16/Z
Wellcome TrustUnited Kingdom218579/Z/19/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V018523/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Database references