8CD0 | pdb_00008cd0

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

• PDB DOI: https://doi.org/10.2210/pdb8CD0/pdb
• EM Map EMD-16565: EMDB EMDataResource

• Classification: CARBOHYDRATE
• Organism(s): Homo sapiens, Lama glama
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-29 Released: 2024-02-07 
• Deposition Author(s): Mycroft-West, C.J., Wu, L.
• Funding Organization(s): Engineering and Physical Sciences Research Council, Wellcome Trust, Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

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

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

• PubMed: 38351061 
• DOI: https://doi.org/10.1038/s41467-024-45419-4
• Primary Citation 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.

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Organizational Affiliation: 
• The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK.
Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK.
Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
School of Chemistry and Physics, Queensland University of Technology, QLD 4000, Brisbane, Australia.
Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia.
Centre for Glycoscience Research and Training, Keele University, ST5 5BG, Newcastle-Under-Lyme, UK.
The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK. [e-mail].
Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 119.12 kDa 
• Atom Count: 6,860 
• Modeled Residue Count: 837 
• Deposited Residue Count: 1,044 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1	A	882	Homo sapiens	Mutation(s): 0  Gene Names: NDST1, HSST, HSST1 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody nAb7	B [auth C]	162	Lama glama	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A3P (Subject of Investigation/LOI)	C [auth A]	ADENOSINE-3'-5'-DIPHOSPHATE C10 H15 N5 O10 P2 WHTCPDAXWFLDIH-KQYNXXCUSA-N
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Mycroft-West, C.J., Wu, L.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--
Wellcome Trust	United Kingdom	060208/Z/00/Z
Wellcome Trust	United Kingdom	093305/Z/10/Z
Wellcome Trust	United Kingdom	203141/Z/16/Z
Wellcome Trust	United Kingdom	218579/Z/19/Z
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/V018523/1

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references
• Version 1.2: 2024-10-09
  Changes: Data collection, Structure summary