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Catalytic Site Atlas Version 2.2.12
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CSA entry for 1nlu
Original Entry
Title:
Hydrolase
Compound:
Sedolisin
Mutant:
No
UniProt/Swiss-Prot:
P42790-PICP_PSESR
EC Class:
3.4.21.100
Other CSA Entries:
Overview of all sites for 1nlu
Homologues of 1nlu
Entries for UniProt/Swiss-Prot: P42790
Entries for EC: 3.4.21.100
Other Databases:
PDB entry: 1nlu
PDBsum entry: 1nlu
UniProt/Swiss-Prot: P42790
IntEnz entry: 3.4.21.100
Literature Report:
Introduction:
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.
Mechanism:
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.
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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
GLUA 80 295Sidechain
Acid/baseResidue
Involved in proton relay, and activates Ser 287 to allow it to act as a nucleophile in attack of the protein's scissile bond.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12673349 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12673349 Current protein Structural similarity to homologue of known mechanism
PubMed ID 12673349 Current protein Conservation of residue
PubMed ID 1562589 Current protein pH dependence of reaction

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 84 299Sidechain
Acid/baseResidue
Involved in proton transfer system and activates Glu 80.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12673349 Current protein Conservation of residue
PubMed ID 10488127 Current protein Mutagenesis of residue
PubMed ID 1562589 Current protein pH dependence of reaction
PubMed ID 12673349 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12673349 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASPA 170 385Sidechain
ElectrostaticTransition state
Forms the oxyanion hole and stabilises the tetrahedral transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12673349 Current protein Structural similarity to homologue of known mechanism
PubMed ID 10488127 Current protein Mutagenesis of residue
PubMed ID 12673349 Current protein Conservation of residue
PubMed ID 12673349 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
SERA 287 502Sidechain
NucleophileSubstrate
Acts as a nucleophile to attack the scissile bond in the polypeptide.
Evidence from paper Evidence concerns Evidence type
PubMed ID 12673349 Current protein Structural similarity to homologue of known mechanism
PubMed ID 12673349 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 12673349 Current protein Residue is covalently bound to intermediate, based on structural data
PubMed ID 12673349 Current protein Conservation of residue
References:
1
Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases.
A. Wlodawer and M. Li and A. Gustchina and H. Oyama and B. M. Dunn and K. Oda
Acta Biochim Pol 50, (1) 81-102, (2003).
12673349
2
Substrate specificity and kinetic properties of pepstatin-insensitive carboxyl proteinase from Pseudomonas sp. No. 101.
K. Oda and H. Nakatani and B. M. Dunn
Biochim Biophys Acta 1120, (2) 208-14, (1992).
1562589
3
Identification of catalytic residues of pepstatin-insensitive carboxyl proteinases from prokaryotes by site-directed mutagenesis.
H. Oyama and S. Abe and S. Ushiyama and S. Takahashi and K. Oda
J Biol Chem 274, (39) 27815-22, (1999).
10488127
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