[English] 日本語
Yorodumi- PDB-9s6b: Aeropyrum pernix acylaminoacyl peptidase co-crystallized with mer... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 9s6b | |||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Title | Aeropyrum pernix acylaminoacyl peptidase co-crystallized with meropenem. | |||||||||||||||
Components | Acylamino-acid-releasing enzyme | |||||||||||||||
Keywords | HYDROLASE / serine protease / HbPG / ligand binding | |||||||||||||||
| Function / homology | Function and homology informationacylaminoacyl-peptidase / omega peptidase activity / serine-type endopeptidase activity / proteolysis / cytoplasm Similarity search - Function | |||||||||||||||
| Biological species | ![]() Aeropyrum pernix K1 (archaea) | |||||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | |||||||||||||||
Authors | Harmat, V. / Takacs, L. / Kiss-Szeman, A. / Banoczi, Z. / Jakli, I. / Hosogi, N. / Traore, D.A.K. / Perczel, A. / Menyhard, D.K. | |||||||||||||||
| Funding support | European Union, Hungary, 4items
| |||||||||||||||
Citation | Journal: Protein Sci / Year: 2025Title: Ligand binding Pro-miscuity of acylpeptide hydrolase, structural analysis of a detoxifying serine hydrolase. Authors: Anna J Kiss-Szemán / Luca Takács / Imre Jákli / Zoltán Bánóczi / Naoki Hosogi / Daouda A K Traore / Veronika Harmat / András Perczel / Dóra K Menyhárd / ![]() Abstract: 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 ...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. | |||||||||||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 9s6b.cif.gz | 1012.8 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb9s6b.ent.gz | 703 KB | Display | PDB format |
| PDBx/mmJSON format | 9s6b.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9s6b_validation.pdf.gz | 468.1 KB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 9s6b_full_validation.pdf.gz | 482.1 KB | Display | |
| Data in XML | 9s6b_validation.xml.gz | 87.3 KB | Display | |
| Data in CIF | 9s6b_validation.cif.gz | 112.2 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/9s6b ftp://data.pdbj.org/pub/pdb/validation_reports/s6/9s6b | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9gneC ![]() 9gouC ![]() 9hxqC C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
Movie
Controller
Components
About Yorodumi




Aeropyrum pernix K1 (archaea)
X-RAY DIFFRACTION
Hungary, 4items
Citation








PDBj


