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Structure paper

TitlePlatform-directed allostery and quaternary structure dynamics of SAMHD1 catalysis.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 3775, Year 2024
Publish dateMay 6, 2024
AuthorsOliver J Acton / Devon Sheppard / Simone Kunzelmann / Sarah J Caswell / Andrea Nans / Ailidh J O Burgess / Geoff Kelly / Elizabeth R Morris / Peter B Rosenthal / Ian A Taylor /
PubMed AbstractSAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T- ...SAMHD1 regulates cellular nucleotide homeostasis, controlling dNTP levels by catalysing their hydrolysis into 2'-deoxynucleosides and triphosphate. In differentiated CD4+ macrophage and resting T-cells SAMHD1 activity results in the inhibition of HIV-1 infection through a dNTP blockade. In cancer, SAMHD1 desensitizes cells to nucleoside-analogue chemotherapies. Here we employ time-resolved cryogenic-EM imaging and single-particle analysis to visualise assembly, allostery and catalysis by this multi-subunit enzyme. Our observations reveal how dynamic conformational changes in the SAMHD1 quaternary structure drive the catalytic cycle. We capture five states at high-resolution in a live catalytic reaction, revealing how allosteric activators support assembly of a stable SAMHD1 tetrameric core and how catalysis is driven by the opening and closing of active sites through pairwise coupling of active sites and order-disorder transitions in regulatory domains. This direct visualisation of enzyme catalysis dynamics within an allostery-stabilised platform sets a precedent for mechanistic studies into the regulation of multi-subunit enzymes.
External linksNat Commun / PubMed:38710701 / PubMed Central
MethodsEM (single particle)
Resolution2.65 - 3.43 Å
Structure data

18729

8qxj

EMDB-18729, PDB-8qxj:
Cryo-EM structure of tetrameric human SAMHD1 with dApNHpp
Method: EM (single particle) / Resolution: 2.65 Å

18730

8qxk

EMDB-18730, PDB-8qxk:
Cryo-EM structure of tetrameric human SAMHD1 State I - Tense
Method: EM (single particle) / Resolution: 2.66 Å

18731

8qxl

EMDB-18731, PDB-8qxl:
Cryo-EM structure of tetrameric human SAMHD1 State II - Hemi-relaxed
Method: EM (single particle) / Resolution: 2.82 Å

18732

8qxm

EMDB-18732, PDB-8qxm:
Cryo-EM structure of tetrameric human SAMHD1 State III - Relaxed
Method: EM (single particle) / Resolution: 2.94 Å

18733

8qxn

EMDB-18733, PDB-8qxn:
Cryo-EM structure of tetrameric human SAMHD1 State IV - Depleted relaxed
Method: EM (single particle) / Resolution: 2.98 Å

18734

8qxo

EMDB-18734, PDB-8qxo:
Cryo-EM structure of tetrameric human SAMHD1 State V - Depleted relaxed
Method: EM (single particle) / Resolution: 3.43 Å

Chemicals

ChemComp-DZ4:
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine

ChemComp-FE:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

ChemComp-HOH:
WATER

ChemComp-DCP:
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

ChemComp-DCZ:
2'-DEOXYCYTIDINE

ChemComp-3PO:
TRIPHOSPHATE

Source
  • homo sapiens (human)
KeywordsHYDROLASE / TRIPHOSPHOHYDROLASE / METALLO-ENZYME / BINUCLEAR / HD

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