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TitleMolecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 8, Year 2024
Publish dateJan 2, 2024
AuthorsJingjing Hong / Tingting Li / Yulin Chao / Yidan Xu / Zhini Zhu / Zixuan Zhou / Weijie Gu / Qianhui Qu / Dianfan Li /
PubMed AbstractThe secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates ...The secretion and quality control of glycosylphosphatidylinositol-anchored proteins (GPI-APs) necessitates post-attachment remodeling initiated by the evolutionarily conserved PGAP1, which deacylates the inositol in nascent GPI-APs. Impairment of PGAP1 activity leads to developmental diseases in humans and fatality and infertility in animals. Here, we present three PGAP1 structures (2.66-2.84 Å), revealing its 10-transmembrane architecture and product-enzyme interaction details. PGAP1 holds GPI-AP acyl chains in an optimally organized, guitar-shaped cavity with apparent energetic penalties from hydrophobic-hydrophilic mismatches. However, abundant glycan-mediated interactions in the lumen counterbalance these repulsions, likely conferring substrate fidelity and preventing off-target hydrolysis of bulk membrane lipids. Structural and biochemical analyses uncover a serine hydrolase-type catalysis with atypical features and imply mechanisms for substrate entrance and product release involving a drawing compass movement of GPI-APs. Our findings advance the mechanistic understanding of GPI-AP remodeling.
External linksNat Commun / PubMed:38167496 / PubMed Central
MethodsEM (single particle)
Resolution2.66 - 2.84 Å
Structure data

36995

8k9q

EMDB-36995, PDB-8k9q:
Cryo-EM structure of the GPI inositol-deacylase (PGAP1/Bst1) from Chaetomium thermophilum
Method: EM (single particle) / Resolution: 2.84 Å

36996

8k9r

EMDB-36996, PDB-8k9r:
Cryo EM structure of the products-bound PGAP1(Bst1)-H443N from Chaetomium thermophilum
Method: EM (single particle) / Resolution: 2.68 Å

36997

8k9t

EMDB-36997, PDB-8k9t:
Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum
Method: EM (single particle) / Resolution: 2.66 Å

Chemicals

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-D39:
(2~{S})-2-azanyl-3-[[(2~{R})-3-hexadecanoyloxy-2-[(~{Z})-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-propanoic acid

ChemComp-MAN:
alpha-D-mannopyranose

ChemComp-05E:
2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate

ChemComp-PA1:
2-amino-2-deoxy-alpha-D-glucopyranose

ChemComp-L9H:
[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] octadecanoate

ChemComp-PLM:
PALMITIC ACID

ChemComp-CLR:
CHOLESTEROL

ChemComp-80Y:
2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate

ChemComp-LYI:
[(2~{R})-1-octadecoxy-3-[oxidanyl-[(2~{R},3~{R},5~{S},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z},11~{Z},14~{Z})-icosa-5,8,11,14-tetraenoate

Source
  • Thermochaetoides thermophila (fungus)
  • synthetic construct (others)
  • chaetomium thermophilum (strain dsm 1495 / cbs 144.50 / imi 039719) (fungus)
  • psychromonas sp. b3m02 (bacteria)
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / Bst1 / Glycosylphosphatidylinositol / GPI anchoring / GPI-AP / GPI-AP remodelase / Integral membrane enzyme / Lipase / Lipid remodeling / Membrane enzyme / Nanodisc / PGAP1 / Transmembrane enzyme / Triad enzyme / TGP / Thermostable green fluorescence protein / Triad enzyme.

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