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TitleStructure-based mechanism of riboregulation of the metabolic enzyme SHMT1.
Journal, issue, pagesMol Cell, Vol. 84, Issue 14, Page 2682-22697.e6, Year 2024
Publish dateJul 25, 2024
AuthorsSharon Spizzichino / Federica Di Fonzo / Chiara Marabelli / Angela Tramonti / Antonio Chaves-Sanjuan / Alessia Parroni / Giovanna Boumis / Francesca Romana Liberati / Alessio Paone / Linda Celeste Montemiglio / Matteo Ardini / Arjen J Jakobi / Alok Bharadwaj / Paolo Swuec / Gian Gaetano Tartaglia / Alessandro Paiardini / Roberto Contestabile / Antonello Mai / Dante Rotili / Francesco Fiorentino / Alberto Macone / Alessandra Giorgi / Giancarlo Tria / Serena Rinaldo / Martino Bolognesi / Giorgio Giardina / Francesca Cutruzzolà /
PubMed AbstractRNA can directly control protein activity in a process called riboregulation; only a few mechanisms of riboregulation have been described in detail, none of which have been characterized on ...RNA can directly control protein activity in a process called riboregulation; only a few mechanisms of riboregulation have been described in detail, none of which have been characterized on structural grounds. Here, we present a comprehensive structural, functional, and phylogenetic analysis of riboregulation of cytosolic serine hydroxymethyltransferase (SHMT1), the enzyme interconverting serine and glycine in one-carbon metabolism. We have determined the cryoelectron microscopy (cryo-EM) structure of human SHMT1 in its free- and RNA-bound states, and we show that the RNA modulator competes with polyglutamylated folates and acts as an allosteric switch, selectively altering the enzyme's reactivity vs. serine. In addition, we identify the tetrameric assembly and a flap structural motif as key structural elements necessary for binding of RNA to eukaryotic SHMT1. The results presented here suggest that riboregulation may have played a role in evolution of eukaryotic SHMT1 and in compartmentalization of one-carbon metabolism. Our findings provide insights for RNA-based therapeutic strategies targeting this cancer-linked metabolic pathway.
External linksMol Cell / PubMed:38996576
MethodsEM (single particle)
Resolution3.29 - 3.52 Å
Structure data

15065

8a11

EMDB-15065, PDB-8a11:
Cryo-EM structure of the Human SHMT1-RNA complex
Method: EM (single particle) / Resolution: 3.52 Å

18973

8r7h

EMDB-18973, PDB-8r7h:
Cryo-EM structure of Human SHMT1
Method: EM (single particle) / Resolution: 3.29 Å

Chemicals

ChemComp-PLP:
PYRIDOXAL-5'-PHOSPHATE

Source
  • homo sapiens (human)
KeywordsTRANSFERASE / Riboregulation / Metabolism / 1 carbon metablism / Moonlighting protein / RNA BINDING PROTEIN / Serine / Glycine Metabolism

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