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TitleStructure of substrate-bound SMG1-8-9 kinase complex reveals molecular basis for phosphorylation specificity.
Journal, issue, pagesElife, Vol. 9, Year 2020
Publish dateMay 29, 2020
AuthorsLukas M Langer / Yair Gat / Fabien Bonneau / Elena Conti /
PubMed AbstractPI3K-related kinases (PIKKs) are large Serine/Threonine (Ser/Thr)-protein kinases central to the regulation of many fundamental cellular processes. PIKK family member SMG1 orchestrates progression of ...PI3K-related kinases (PIKKs) are large Serine/Threonine (Ser/Thr)-protein kinases central to the regulation of many fundamental cellular processes. PIKK family member SMG1 orchestrates progression of an RNA quality control pathway, termed nonsense-mediated mRNA decay (NMD), by phosphorylating the NMD factor UPF1. Phosphorylation of UPF1 occurs in its unstructured N- and C-terminal regions at Serine/Threonine-Glutamine (SQ) motifs. How SMG1 and other PIKKs specifically recognize SQ motifs has remained unclear. Here, we present a cryo-electron microscopy (cryo-EM) reconstruction of a human SMG1-8-9 kinase complex bound to a UPF1 phosphorylation site at an overall resolution of 2.9 Å. This structure provides the first snapshot of a human PIKK with a substrate-bound active site. Together with biochemical assays, it rationalizes how SMG1 and perhaps other PIKKs specifically phosphorylate Ser/Thr-containing motifs with a glutamine residue at position +1 and a hydrophobic residue at position -1, thus elucidating the molecular basis for phosphorylation site recognition.
External linksElife / PubMed:32469312 / PubMed Central
MethodsEM (single particle)
Resolution2.97 Å
Structure data

11063

6z3r

EMDB-11063, PDB-6z3r:
Structure of SMG1-8-9 kinase complex bound to UPF1-LSQ
Method: EM (single particle) / Resolution: 2.97 Å

Chemicals

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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

ChemComp-MG:
Unknown entry

Source
  • homo sapiens (human)
KeywordsTRANSFERASE / Cryo-EM / Structural Biology / Nonsense-mediated mRNA decay / RNA quality control / PIKK / NMD / Substrate / Phosphorylation

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