Scytalidopepsin B

 

Scytalidopepsin-B is a member of a group of fungal pepstatin-insensitive glutamic peptidases known as the eqolsins. The enzyme has been shown to cleave angiotensin II and the oxidised insulin B chain, and operates most efficiently in acidic conditions. The eqolsins show no sequence homology to the well known pepsin-like or retroviral aspartic peptidases.

 

Reference Protein and Structure

Sequence
P15369 UniProt (3.4.23.32) IPR033863 (Sequence Homologues) (PDB Homologues)
Biological species
Scytalidium lignicola (Fungus) Uniprot
PDB
1s2k - Structure of SCP-B a member of the Eqolisin family of Peptidases in a complex with a Tripeptide Ala-Ile-His (2.0 Å) PDBe PDBsum 1s2k
Catalytic CATH Domains
2.60.120.700 CATHdb (see all for 1s2k)
Click To Show Structure

Enzyme Reaction (EC:3.4.23.32)

Phe-Phe
CHEBI:72723ChEBI
+
water
CHEBI:15377ChEBI
→
L-phenylalanine
CHEBI:17295ChEBI
Alternative enzyme names: Ganoderma lucidum aspartic proteinase, Ganoderma lucidum carboxyl proteinase, Scytalidium lignicolum aspartic proteinase B, Scytalidium aspartic proteinase B, SLB,

Enzyme Mechanism

Introduction

Glu 136 removes a proton from a water molecule which acts as a nucleophile to attack the peptide carbonyl. The tetrahedral intermediate and transition state leading to it is stabilised by hydrogen bonding from the side chain amide of Gln 53. Collapse of the intermediate with protonation of the departing nitrogen by Glu 136 completes the reaction.

Catalytic Residues Roles

UniProt PDB* (1s2k)
Gln107 Gln53A Stabilises the tetrahedral intermediate/transition state. electrostatic stabiliser
Glu190 Glu136A Removes a proton from a water molecule which then attacks the peptide carbonyl. Later protonates the departing amine leaving group. proton acceptor, proton donor
*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

proton transfer, bimolecular nucleophilic addition, intermediate formation, overall reactant used, rate-determining step, unimolecular elimination by the conjugate base, intermediate collapse, heterolysis, overall product formed, native state of enzyme regenerated

References

  1. Fujinaga M et al. (2004), Proc Natl Acad Sci U S A, 101, 3364-3369. The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum. DOI:10.1073/pnas.0400246101. PMID:14993599.
  2. Pillai B et al. (2007), J Mol Biol, 365, 343-361. Crystal structure of scytalidoglutamic peptidase with its first potent inhibitor provides insights into substrate specificity and catalysis. DOI:10.1016/j.jmb.2006.09.058. PMID:17069854.
  3. Kataoka Y et al. (2005), FEBS Lett, 579, 2991-2994. Catalytic residues and substrate specificity of scytalidoglutamic peptidase, the first member of the eqolisin in family (G1) of peptidases. DOI:10.1016/j.febslet.2005.04.050. PMID:15907842.

Step 1. Glu136 abstracts a proton from water which activates it to nucleophilically attack the carbonyl carbon.

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Catalytic Residues Roles

Residue Roles
Gln53A electrostatic stabiliser
Glu136A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used, rate-determining step

Step 2. The amide nitrogen is protonated by Glu136 which initiates an elimination from the oxyanion which results in the cleavage of the peptide bond.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln53A electrostatic stabiliser
Glu136A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, heterolysis, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu136 abstracts a proton from water which activates it to nucleophilically attack the carbonyl carbon.

Step 2. The amide nitrogen is protonated by Glu136 which initiates an elimination from the oxyanion which results in the cleavage of the peptide bond.

Products.

Contributors

Steven Smith, Gemma L. Holliday, Charity Hornby