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TitleHuman PRPS1 filaments stabilize allosteric sites to regulate activity.
Journal, issue, pagesNat Struct Mol Biol, Vol. 30, Issue 3, Page 391-402, Year 2023
Publish dateFeb 6, 2023
AuthorsKelli L Hvorecny / Kenzee Hargett / Joel D Quispe / Justin M Kollman /
PubMed AbstractThe universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and ...The universally conserved enzyme phosphoribosyl pyrophosphate synthetase (PRPS) assembles filaments in evolutionarily diverse organisms. PRPS is a key regulator of nucleotide metabolism, and mutations in the human enzyme PRPS1 lead to a spectrum of diseases. Here we determine structures of human PRPS1 filaments in active and inhibited states, with fixed assembly contacts accommodating both conformations. The conserved assembly interface stabilizes the binding site for the essential activator phosphate, increasing activity in the filament. Some disease mutations alter assembly, supporting the link between filament stability and activity. Structures of active PRPS1 filaments turning over substrate also reveal coupling of catalysis in one active site with product release in an adjacent site. PRPS1 filaments therefore provide an additional layer of allosteric control, conserved throughout evolution, with likely impact on metabolic homeostasis. Stabilization of allosteric binding sites by polymerization adds to the growing diversity of assembly-based enzyme regulatory mechanisms.
External linksNat Struct Mol Biol / PubMed:36747094 / PubMed Central
MethodsEM (single particle)
Resolution2.0 - 3.2 Å
Structure data

EMDB-27279, PDB-8dbc:
Human PRPS1 with Phosphate; Hexamer
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-27280, PDB-8dbd:
Human PRPS1 with Phosphate; Filament Interface
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-27281, PDB-8dbe:
Human PRPS1 with ADP; Hexamer
Method: EM (single particle) / Resolution: 2.1 Å

EMDB-27282, PDB-8dbf:
Human PRPS1 with ADP; Filament Interface
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-27283, PDB-8dbg:
Human PRPS1 with Phosphate and ATP; Hexamer
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-27284, PDB-8dbh:
Human PRPS1 with Phosphate and ATP; Filament Interface
Method: EM (single particle) / Resolution: 2.2 Å

EMDB-27285, PDB-8dbi:
Human PRPS1 with Phosphate, ATP, and R5P; Hexamer
Method: EM (single particle) / Resolution: 2.0 Å

EMDB-27286, PDB-8dbj:
Human PRPS1 with Phosphate, ATP, and R5P; Filament Interface
Method: EM (single particle) / Resolution: 2.0 Å

EMDB-27287, PDB-8dbk:
Human PRPS1 with Phosphate, ATP, and R5P; Hexamer with resolved catalytic loops
Method: EM (single particle) / Resolution: 2.1 Å

EMDB-27288: Human PRPS1 with Phosphate, ATP, and R5P; Hexamer with resolved catalytic loops
Method: EM (single particle) / Resolution: 2.1 Å

EMDB-27289, PDB-8dbl:
Human PRPS1 with Phosphate and PRPP; Hexamer
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-27290, PDB-8dbm:
Human PRPS1 with Phosphate and PRPP; Filament Interface
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-27291, PDB-8dbn:
Human PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P; Hexamer
Method: EM (single particle) / Resolution: 2.4 Å

EMDB-27292: Human PRPS1-E307A engineered mutation with Phosphate, ATP, and R5P; Symmetry-expanded Hexamer
Method: EM (single particle) / Resolution: 2.6 Å

EMDB-27293, PDB-8dbo:
Human PRPS1-E307A engineered mutation with ADP; Hexamer
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-27294: Human PRPS1-E307A engineered mutation with ADP; Symmetry-expanded Hexamer 1
Method: EM (single particle) / Resolution: 2.5 Å

EMDB-27295: Human PRPS1-E307A engineered mutation with ADP; Symmetry-expanded Hexamer 2
Method: EM (single particle) / Resolution: 2.6 Å

Chemicals

ChemComp-PO4:
PHOSPHATE ION

ChemComp-HSX:
5-O-phosphono-alpha-D-ribofuranose

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

ChemComp-PRP:
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

Source
  • homo sapiens (human)
KeywordsTRANSFERASE / phosphoribosyl pyrophosphate synthetase / phosphate / phosphate activator / ADP inhibitor / ATP substrate / ATP and R5P substrates / catalytic loop / PRPP product / ATP/R5P substrate / Filament-breaking mutation

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