8K9T | pdb_00008k9t

Cryo-EM structure of the products-bound PGAP1(Bst1)-S327A from Chaetonium thermophilum

PDB DOI: https://doi.org/10.2210/pdb8K9T/pdb
EM Map EMD-36997: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Thermochaetoides thermophila DSM 1495, Psychromonas sp. B3M02, synthetic construct, Homo sapiens
Expression System: Homo sapiens
Mutation(s): Yes
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2023-08-01 Released: 2023-12-20
Deposition Author(s): Li, T., Hong, J., Qu, Q., Li, D.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Molecular basis of the inositol deacylase PGAP1 involved in quality control of GPI-AP biogenesis.

Hong, J., Li, T., Chao, Y., Xu, Y., Zhu, Z., Zhou, Z., Gu, W., Qu, Q., Li, D.

(2024) Nat Commun 15: 8-8

PubMed: 38167496 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-44568-2
Primary Citation Related Structures:
8K9Q, 8K9R, 8K9T

PubMed Abstract:
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.

Organizational Affiliation

State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.

Macromolecule Content

Total Structure Weight: 194.29 kDa
Atom Count: 7,747
Modeled Residue Count: 965
Deposited Residue Count: 1,719
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GPI inositol-deacylase,MCherry protein	A	1,447	Thermochaetoides thermophila DSM 1495, Psychromonas sp. B3M02 This entity is chimeric	Mutation(s): 5 Gene Names: CTHT_0034210, DS885_16260 EC: 3.1 Membrane Entity: Yes
UniProt
Find proteins for G0S652 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)) Explore G0S652 Go to UniProtKB: G0S652
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	G0S652
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein,Complement decay-accelerating factor	B	272	synthetic construct, Homo sapiens This entity is chimeric	Mutation(s): 0 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P08174 (Homo sapiens) Explore P08174 Go to UniProtKB: P08174
PHAROS: P08174 GTEx: ENSG00000196352
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08174
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LYI (Subject of Investigation/LOI) Query on LYI Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	[(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 C₄₇ H₈₅ O₁₂ P WVZYOWMZDZYUMR-MCRWXTICSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	I [auth A], J [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A]
80Y (Subject of Investigation/LOI) Query on 80Y Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-azanylethyl [(2R,3S,4S,5S,6S)-3,4,5,6-tetrakis(oxidanyl)oxan-2-yl]methyl hydrogen phosphate C₈ H₁₈ N O₉ P MMKGFVVPDOLYRA-HEIBUPTGSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
05E (Subject of Investigation/LOI) Query on 05E Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	2-azanylethyl [(2~{S},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl] hydrogen phosphate C₈ H₁₈ N O₉ P AMJFTSXJOORFJX-HEIBUPTGSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MAN (Subject of Investigation/LOI) Query on MAN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
PA1 (Subject of Investigation/LOI) Query on PA1 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	2-amino-2-deoxy-alpha-D-glucopyranose C₆ H₁₃ N O₅ MSWZFWKMSRAUBD-UKFBFLRUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]