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TitleBiochemical and structural characterization of Rab3GAP reveals insights into Rab18 nucleotide exchange activity.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 479, Year 2025
Publish dateJan 8, 2025
AuthorsGage M J Fairlie / Kha M Nguyen / Sung-Eun Nam / Alexandria L Shaw / Matthew A H Parson / Hannah R Shariati / Xinyin Wang / Meredith L Jenkins / Michael Gong / John E Burke / Calvin K Yip /
PubMed AbstractThe heterodimeric Rab3GAP complex is a guanine nucleotide exchange factor (GEF) for the Rab18 GTPase that regulates lipid droplet metabolism, ER-to-Golgi trafficking, secretion, and autophagy. Why ...The heterodimeric Rab3GAP complex is a guanine nucleotide exchange factor (GEF) for the Rab18 GTPase that regulates lipid droplet metabolism, ER-to-Golgi trafficking, secretion, and autophagy. Why both subunits of Rab3GAP are required for Rab18 GEF activity and the molecular basis of how Rab3GAP engages and activates its cognate substrate are unknown. Here we show that human Rab3GAP is conformationally flexible and potentially autoinhibited by the C-terminal domain of its Rab3GAP2 subunit. Our high-resolution structure of the catalytic core of Rab3GAP, determined by cryo-EM, shows that the Rab3GAP2 N-terminal domain binds Rab3GAP1 via an extensive interface. AlphaFold3 modelling analysis together with targeted mutagenesis and in vitro activity assay reveal that Rab3GAP likely engages its substrate Rab18 through an interface away from the switch and interswitch regions. Lastly, we find that three Warburg Micro Syndrome-associated missense mutations do not affect the overall architecture of Rab3GAP but instead likely interfere with substrate binding.
External linksNat Commun / PubMed:39779760 / PubMed Central
MethodsEM (single particle)
Resolution3.37 - 3.39 Å
Structure data

EMDB-43645: Cryo-EM structure of human core Rab3GAP1/2 complex
Method: EM (single particle) / Resolution: 3.39 Å

43655

8vyb

EMDB-43655: Cryo-EM structure of human core Rab3GAP1/2 complex, local refinement
PDB-8vyb: Cryo-EM structure of human core Rab3GAP1/2 complex
Method: EM (single particle) / Resolution: 3.37 Å

Source
  • homo sapiens (human)
KeywordsCYTOSOLIC PROTEIN / Complex / GAP / GEF / Rab3GAP / Lipid droplet / ER / Rab regulator / membrane trafficking

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