Sedolisin
Sedolisins are proteolytic enzymes resembling subtilisin. They are a related family of serine-carboxyl peptidases with a unique Ser-Glu-Asp catalytic triad and require calcium ions to maintain structural integrity.
Reference Protein and Structure
- Sequence
-
P42790
(3.4.21.100)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Pseudomonas sp. 101 (Bacteria)
- PDB
-
1nlu
- Pseudomonas sedolisin (serine-carboxyl proteinase) complexed with two molecules of pseudo-iodotyrostatin
(1.3 Å)
- Catalytic CATH Domains
-
3.40.50.200
(see all for 1nlu)
- Cofactors
- Calcium(2+) (1)
Enzyme Reaction (EC:3.4.21.100)
+
→
Alternative enzyme names: Pseudomonas sp. pepstatin-insensitive carboxyl proteinase, Pseudomonapepsin, Pseudomonalisin, Sedolysin,
Enzyme Mechanism
Introduction
Ser 287 acts as a nucleophile to attack the scissile bond and form an acyl-enzyme intermediate. Glu 80 interacts with Ser 287, and Asp 84 in turn with Glu 80. A chain of proton donors originates with a bound water molecule interacting with protonated Asp 84. In turn, this residue interacts with protonated Glu 80, which donates a proton to Ser 287. A water molecule accepts protons from Ser 287, and protonated Asp 170 which forms the oxyanion hole stabilising the tetrahedral intermediate.
Catalytic Residues Roles
| UniProt | PDB* (1nlu) | ||
| Glu295 | Glu80A | Involved in proton relay, and activates Ser 287 to allow it to act as a nucleophile in attack of the protein's scissile bond. | proton shuttle (general acid/base) |
| Asp385 | Asp170A | Forms the oxyanion hole and stabilises the tetrahedral transition state. | electrostatic stabiliser |
| Asp299 | Asp84A | Involved in proton transfer system and activates Glu 80. | proton shuttle (general acid/base) |
| Ser502 | Ser287A | Acts as a nucleophile to attack the scissile bond in the polypeptide | covalent catalysis |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Ekici OD et al. (2008), Protein Sci, 17, 2023-2037. Unconventional serine proteases: Variations on the catalytic Ser/His/Asp triad configuration. DOI:10.1110/ps.035436.108. PMID:18824507.
- Oda K (2012), J Biochem, 151, 13-25. New families of carboxyl peptidases: serine-carboxyl peptidases and glutamic peptidases. DOI:10.1093/jb/mvr129. PMID:22016395.
- Wlodawer A et al. (2004), Biochem Biophys Res Commun, 314, 638-645. Two inhibitor molecules bound in the active site of Pseudomonas sedolisin: a model for the bi-product complex following cleavage of a peptide substrate. DOI:10.1016/j.bbrc.2003.12.130.
- Wlodawer A et al. (2003), Acta Biochim Pol, 50, 81-102. Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases. DOI:035001081. PMID:12673349.
- Wlodawer A et al. (2001), Nat Struct Biol, 8, 442-446. Carboxyl proteinase from Pseudomonas defines a novel family of subtilisin-like enzymes. DOI:10.1038/87610. PMID:11323721.
- Oyama H et al. (1999), J Biol Chem, 274, 27815-27822. Identification of Catalytic Residues of Pepstatin-insensitive Carboxyl Proteinases from Prokaryotes by Site-directed Mutagenesis. DOI:10.1074/jbc.274.39.27815. PMID:10488127.
- Oda K et al. (1992), Biochim Biophys Acta, 1120, 208-214. Substrate specificity and kinetic properties of pepstatin-insensitive carboxyl proteinase from Pseudomanas sp. No. 101. DOI:10.1016/0167-4838(92)90272-f. PMID:1562589.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Glu80A | proton shuttle (general acid/base) |
| Asp170A | electrostatic stabiliser |
| Ser287A | covalent catalysis |
| Asp84A | proton shuttle (general acid/base) |