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- EMDB-16564: Human heparan sulfate N-deacetylase-N-sulfotransferase 1 in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-16564
TitleHuman heparan sulfate N-deacetylase-N-sulfotransferase 1 in complex with calcium and 3'-phosphoadenosine-5'-phosphosulfate
Map data
Sample
  • Complex: Human heparan sulfate N-deacetylase-N-sulfotransferase 1
    • Protein or peptide: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
  • Ligand: ADENOSINE-3'-5'-DIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: water
KeywordsDeacetylase / Sulfotransferase / Heparan Sulfate / Carbohydrate / Glycosaminoglycan
Function / homology
Function and homology information


[heparan sulfate]-glucosamine N-sulfotransferase / heparan sulfate N-sulfotransferase activity / heparan sulfate N-deacetylase activity / N-acetylglucosamine deacetylase activity / heparin proteoglycan biosynthetic process / embryonic neurocranium morphogenesis / embryonic viscerocranium morphogenesis / HS-GAG biosynthesis / deacetylase activity / cardiac septum development ...[heparan sulfate]-glucosamine N-sulfotransferase / heparan sulfate N-sulfotransferase activity / heparan sulfate N-deacetylase activity / N-acetylglucosamine deacetylase activity / heparin proteoglycan biosynthetic process / embryonic neurocranium morphogenesis / embryonic viscerocranium morphogenesis / HS-GAG biosynthesis / deacetylase activity / cardiac septum development / glycosaminoglycan metabolic process / heparan sulfate proteoglycan biosynthetic process / respiratory gaseous exchange by respiratory system / polysaccharide biosynthetic process / coronary vasculature development / positive regulation of smoothened signaling pathway / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / aorta development / midbrain development / forebrain development / fibroblast growth factor receptor signaling pathway / trans-Golgi network membrane / cell population proliferation / positive regulation of MAPK cascade / inflammatory response / Golgi membrane / Golgi apparatus
Similarity search - Function
Heparan sulphate-N-deacetylase / : / Heparan sulfate-N-deacetylase, deacetylase domain / Heparan sulfate-N-deacetylase, N-terminal domain / Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMycroft-West CJ / Wu L
Funding support United Kingdom, 6 items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
Wellcome Trust203141/Z/16/Z United Kingdom
Wellcome Trust218579/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V018523/1 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1.
Authors: Courtney J Mycroft-West / Sahar Abdelkarim / Helen M E Duyvesteyn / Neha S Gandhi / Mark A Skidmore / Raymond J Owens / Liang Wu /
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, ...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.
History
DepositionJan 28, 2023-
Header (metadata) releaseFeb 7, 2024-
Map releaseFeb 7, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16564.png

Downloads & links

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Map

FileDownload / File: emd_16564.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.42558625 - 0.72343224
Average (Standard dev.)0.00015679449 (±0.009722724)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 321.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16564_msk_1.map
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Half map: #2

Fileemd_16564_half_map_1.map
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Half map: #1

Fileemd_16564_half_map_2.map
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Sample components

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Entire : Human heparan sulfate N-deacetylase-N-sulfotransferase 1

EntireName: Human heparan sulfate N-deacetylase-N-sulfotransferase 1
Components
  • Complex: Human heparan sulfate N-deacetylase-N-sulfotransferase 1
    • Protein or peptide: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
  • Ligand: ADENOSINE-3'-5'-DIPHOSPHATE
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Human heparan sulfate N-deacetylase-N-sulfotransferase 1

SupramoleculeName: Human heparan sulfate N-deacetylase-N-sulfotransferase 1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1

MacromoleculeName: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.407461 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SRTDPLVLVF VESLYSQLGQ EVVAILESSR FKYRTEIAPG KGDMPTLTDK GRGRFALIIY ENILKYVNLD AWNRELLDKY CVAYGVGII GFFKANENSL LSAQLKGFPL FLHSNLGLKD CSINPKSPLL YVTRPSEVEK GVLPGEDWTV FQSNHSTYEP V LLAKTRSS ...String:
SRTDPLVLVF VESLYSQLGQ EVVAILESSR FKYRTEIAPG KGDMPTLTDK GRGRFALIIY ENILKYVNLD AWNRELLDKY CVAYGVGII GFFKANENSL LSAQLKGFPL FLHSNLGLKD CSINPKSPLL YVTRPSEVEK GVLPGEDWTV FQSNHSTYEP V LLAKTRSS ESIPHLGADA GLHAALHATV VQDLGLHDGI QRVLFGNNLN FWLHKLVFVD AVAFLTGKRL SLPLDRYILV DI DDIFVGK EGTRMKVEDV KALFDTQNEL RAHIPNFTFN LGYSGKFFHT GTNAEDAGDD LLLSYVKEFW WFPHMWSHMQ PHL FHNQSV LAEQMALNKK FAVEHGIPTD MGYAVAPHHS GVYPVHVQLY EAWKQVWSIR VTSTEEYPHL KPARYRRGFI HNGI MVLPR QTCGLFTHTI FYNEYPGGSS ELDKIINGGE LFLTVLLNPI SIFMTHLSNY GNDRLGLYTF KHLVRFLHSW TNLRL QTLP PVQLAQKYFQ IFSEEKDPLW QDPCEDKRHK DIWSKEKTCD RFPKLLIIGP QKTGTTALYL FLGMHPDLSS NYPSSE TFE EIQFFNGHNY HKGIDWYMEF FPIPSNTTSD FYFEKSANYF DSEVAPRRAA ALLPKAKVLT ILINPADRAY SWYQHQR AH DDPVALKYTF HEVITAGSDA SSKLRALQNR CLVPGWYATH IERWLSAYHA NQILVLDGKL LRTEPAKVMD MVQKFLGV T NTIDYHKTLA FDPKKGFWCQ LLEGGKTKCL GKSKGRKYPE MDLDSRAFLK DYYRDHNIEL SKLLYKMGQT LPTWLREDL QNTR

UniProtKB: Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1

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Macromolecule #2: ADENOSINE-3'-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-3'-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: A3P
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-A3P:
ADENOSINE-3'-5'-DIPHOSPHATE

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 23 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.4 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE
DetailsMonodisperse sample from size exclusion

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371778
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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