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Structure paper

TitleStructures of liganded glycosylphosphatidylinositol transamidase illuminate GPI-AP biogenesis.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 5520, Year 2023
Publish dateSep 8, 2023
AuthorsYidan Xu / Tingting Li / Zixuan Zhou / Jingjing Hong / Yulin Chao / Zhini Zhu / Ying Zhang / Qianhui Qu / Dianfan Li /
PubMed AbstractMany eukaryotic receptors and enzymes rely on glycosylphosphatidylinositol (GPI) anchors for membrane localization and function. The transmembrane complex GPI-T recognizes diverse proproteins at a ...Many eukaryotic receptors and enzymes rely on glycosylphosphatidylinositol (GPI) anchors for membrane localization and function. The transmembrane complex GPI-T recognizes diverse proproteins at a signal peptide region that lacks consensus sequence and replaces it with GPI via a transamidation reaction. How GPI-T maintains broad specificity while preventing unintentional cleavage is unclear. Here, substrates- and products-bound human GPI-T structures identify subsite features that enable broad proprotein specificity, inform catalytic mechanism, and reveal a multilevel safeguard mechanism against its promiscuity. In the absence of proproteins, the catalytic site is invaded by a locally stabilized loop. Activation requires energetically unfavorable rearrangements that transform the autoinhibitory loop into crucial catalytic cleft elements. Enzyme-proprotein binding in the transmembrane and luminal domains respectively powers the conformational rearrangement and induces a competent cleft. GPI-T thus integrates various weak specificity regions to form strong selectivity and prevent accidental activation. These findings provide important mechanistic insights into GPI-anchored protein biogenesis.
External linksNat Commun / PubMed:37684232 / PubMed Central
MethodsEM (single particle)
Resolution2.85 - 3.22 Å
Structure data

35575

8imx

EMDB-35575, PDB-8imx:
Cryo-EM structure of GPI-T with a chimeric GPI-anchored protein
Method: EM (single particle) / Resolution: 2.85 Å

35576

8imy

EMDB-35576, PDB-8imy:
Cryo-EM structure of GPI-T (inactive mutant) with GPI and proULBP2, a proprotein substrate
Method: EM (single particle) / Resolution: 3.22 Å

Chemicals

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

ChemComp-MG:
Unknown entry

ChemComp-6OU:
[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate / phospholipid*YM

ChemComp-AJP:
Digitonin / detergent*YM

ChemComp-CA:
Unknown entry

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

ChemComp-80T:
[(2R)-1-hexadecanoyloxy-3-[[3-[[(2R)-3-hexadecanoyloxy-2-[(Z)-octadec-9-enoyl]oxy-propoxy]-oxidanyl-phosphoryl]oxy-2-oxidanyl-propoxy]-oxidanyl-phosphoryl]oxy-propan-2-yl] (Z)-octadec-9-enoate

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

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

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-81Q:
[(2R)-1-[[(1S,2R,3R,4S,5S,6R)-2-hexadecanoyloxy-3,4,5,6-tetrakis(oxidanyl)cyclohexyl]oxy-oxidanyl-phosphoryl]oxy-3-octadecoxy-propan-2-yl] (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate

Source
  • homo sapiens (human)
  • clavularia sp. (invertebrata)
  • synthetic construct (others)
KeywordsMEMBRANE PROTEIN / cryo-EM / glycosylphosphatidylinositol / GPI / GPI anchored protein / GPI-AP / membrane protein complex / proprotein

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