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Structure paper

TitleLigand binding Pro-miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase.
Journal, issue, pagesProtein Sci, Vol. 34, Issue 11, Page e70320, Year 2025
Publish dateOct 11, 2025
AuthorsAnna J Kiss-Szemán / Luca Takács / Imre Jákli / Zoltán Bánóczi / Naoki Hosogi / Daouda A K Traore / Veronika Harmat / András Perczel / Dóra K Menyhárd /
PubMed AbstractAcylpeptide hydrolase (APEH) or acylaminoacyl-peptidase (AAP) is a serine hydrolase that regulates protein metabolism. It can also bind to and process unusual substrates, acting as a detoxifier. To ...Acylpeptide hydrolase (APEH) or acylaminoacyl-peptidase (AAP) is a serine hydrolase that regulates protein metabolism. It can also bind to and process unusual substrates, acting as a detoxifier. To better understand its promiscuous specificity, we determined the cryo-EM structures of mammalian APEH complexed with classical serine protease partners: a chloromethyl-ketone (CMK) inhibitor, an organophosphate (OP) pesticide (dichlorvos), and benzenesulfonyl-fluoride. Since CMK derivatives of N-acetylated peptides were suggested to induce apoptosis by inhibiting APEH, while OP complexes may serve as biomarkers of OP exposure and are linked to cognitive enhancement, these complexes carry physiological significance. We identified a unique strand-breaker Pro residue in the hydrolase domain, which relaxes the active site into a partially inactivated but more spacious conformation, transforming the classical serine protease apparatus into a versatile yet potent hydrolysis center with broad specificity, distinguishing the mammalian enzyme not only from other APEHs but also from serine α/β hydrolases sharing essentially the same fold.
External linksProtein Sci / PubMed:41074793 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.3 - 3.2 Å
Structure data

51464

9gne

EMDB-51464, PDB-9gne:
CryoEM structure of mammalian AAP in complex with acetyl-alanyl-chloromethylketone
Method: EM (single particle) / Resolution: 3.2 Å

51501

9gou

EMDB-51501, PDB-9gou:
Cryo-EM structure of acylaminoacyl-peptidase in complex with dichlorvos
Method: EM (single particle) / Resolution: 2.65 Å

52489

9hxq

EMDB-52489, PDB-9hxq:
Cryo-EM structure of acylaminoacyl peptidase (AAP) in covalent complex with inhibitor AEBSF
Method: EM (single particle) / Resolution: 2.8 Å

PDB-9s6b:
Aeropyrum pernix acylaminoacyl peptidase co-crystallized with meropenem.
Method: X-RAY DIFFRACTION / Resolution: 2.3 Å

Chemicals

PDB-1ina:
Unknown entry

PDB-1ing:
INFLUENZA A SUBTYPE N2 NEURAMINIDASE COMPLEXED WITH AROMATIC BANA109 INHIBITOR

ChemComp-AES:
4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE / protease inhibitor*YM

ChemComp-1AX:
(2R,2'R)-3,3'-oxydipropane-1,2-diol

ChemComp-HOH:
WATER

Source
  • Sus scrofa domesticus (domestic pig)
  • sus scrofa (pig)
  • aeropyrum pernix k1 (archaea)
KeywordsHYDROLASE / covalent inhibitor / serine-protease / flexible active site / oligopeptidase / self-assembly / dichlorvos / dimethoxy-phosphate / acyl-peptide-hydrolase / oxidized protein hydrolase / APEH / AARE / AAP / OPH / inhibitor / covalent / acylpeptide hydrolase / acylaminoacyl peptidase / sulphonate / serine protease / HbPG / ligand binding

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