Streptogrisin B
Serine protease B extracted from Streptomyces griseus shows similar active site architecture to the well characterised family of human serine proteases and displays trypsin like specificity for its peptide substrates. It has proved especially useful in analysing the effect of peptide inhibitors such as turkey ovomucoid inhibitor.
Reference Protein and Structure
- Sequences
-
P00777
(3.4.21.81)
P68390
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Streptomyces griseus (Bacteria)
- PDB
-
1ds2
- CRYSTAL STRUCTURE OF SGPB:OMTKY3-COO-LEU18I
(1.7 Å)
- Catalytic CATH Domains
-
2.40.10.10
(see all for 1ds2)
Enzyme Reaction (EC:3.4.21.81)
Enzyme Mechanism
Introduction
Ser 255 acts as the nucleophile to attack the peptide after deprotonation by His 147, forming the oxyanion intermediate, stabilised by hydrogen bonding of the oxyanion hole which is formed by Ser 255 and Gly 253. Protonation of the leaving group by His 147 results in the collapse of the tetrahedral intermediate and the resulting acyl enzyme intermediate is hydrolysed by an activated water molecule to give the products. His 147 is enabled to acted as a general acid/base by the lowering of its pKa through hydrogen bonding to Asp 177 and Ser 270.
Catalytic Residues Roles
| UniProt | PDB* (1ds2) | ||
| Ser270 (main-C) | Ser214(156)E(A) (main-C) | Carbonyl O atom is hydrogen-bonded to His 147 Cɛ1 which lowers His 147 pKa to allow it to act as a general acid/base. | electrostatic stabiliser |
| Ser255 (main-N), Gly253 (main-N) | Ser195(141)E(A) (main-N), Gly193(139)E(A) (main-N) | Forms hydrogen bond to stabilise tetrahedral intermediate via oxyanion hole. | electrostatic stabiliser |
| Ser255 | Ser195(141)E(A) | Acts as nucleophile to attack the electrophilic carbon centre of the peptide substrate to form the tetrahedral intermediate. Stabilises the intermediate by hydrogen bonding from NH group. Subsequent collapse of the tetrahedral intermediate forms a covalent acyl-enzyme intermediate which can be hydrolysed to release the products. | nucleofuge, nucleophile, proton acceptor, proton donor |
| Asp177 | Asp102(63)E(A) | Forms hydrogen bond to His 147 to alter pKa suitably to facilitate its function as a general acid-base. | electrostatic stabiliser |
| His147 | His57(33)E(A) | Acts to increase nucleophilicity of Ser 255 to allow formation of the tetrahedral intermediate. Protonates leaving group to facilitate collapse of the intermediate. Activates water to allow hydrolysis of the acyl-enzyme intermediate. | proton acceptor, proton donor |
Chemical Components
proton transfer, bimolecular nucleophilic addition, intermediate formation, overall reactant used, rate-determining step, unimolecular elimination by the conjugate base, intermediate collapse, overall product formed, native state of enzyme regeneratedReferences
- James MN et al. (1980), J Mol Biol, 139, 423-438. Crystal structure studies and inhibition kinetics of tripeptide chloromethyl ketone inhibitors with Streptomyces griseus protease B. DOI:10.1016/0022-2836(80)90139-4. PMID:6777499.
- Lee TW et al. (2008), Biochim Biophys Acta, 1784, 319-334. 1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB). DOI:10.1016/j.bbapap.2007.11.012. PMID:18157955.
Step 1. His147 deprotonates Ser255 which activates it to attack the carbon of the peptide bond in a nucleophilic addition and form the oxyanion intermediate.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp102(63)E(A) | electrostatic stabiliser |
| Gly193(139)E(A) (main-N) | electrostatic stabiliser |
| Ser195(141)E(A) (main-N) | electrostatic stabiliser |
| Ser214(156)E(A) (main-C) | electrostatic stabiliser |
| His57(33)E(A) | proton acceptor |
| Ser195(141)E(A) | proton donor, nucleophile |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used, rate-determining step
Step 2. Collapse of the tetrahedral intermediate with protonation of the departing amine leaving group by His147 generates an acyl-enzyme intermediate and releases one product.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp102(63)E(A) | electrostatic stabiliser |
| Gly193(139)E(A) (main-N) | electrostatic stabiliser |
| Ser195(141)E(A) (main-N) | electrostatic stabiliser |
| Ser214(156)E(A) (main-C) | electrostatic stabiliser |
| His57(33)E(A) | proton donor |
Chemical Components
ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, overall product formed
Step 3. His147 abstracts a proton from a water which activates it to attack the carbon of the ester bond in a nucleophilic addition.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp102(63)E(A) | electrostatic stabiliser |
| Gly193(139)E(A) (main-N) | electrostatic stabiliser |
| Ser195(141)E(A) (main-N) | electrostatic stabiliser |
| Ser214(156)E(A) (main-C) | electrostatic stabiliser |
| His57(33)E(A) | proton acceptor |
Chemical Components
proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used
Step 4. The tetrahedral intermediate collapses which results in the cleavage of the ester bond releasing Ser255 and the other product. The released Ser255 then accepts a proton from His147 which returns the enzyme to its native state.
Download: Image, Marvin FileCatalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp102(63)E(A) | electrostatic stabiliser |
| Gly193(139)E(A) (main-N) | electrostatic stabiliser |
| Ser195(141)E(A) (main-N) | electrostatic stabiliser |
| Ser214(156)E(A) (main-C) | electrostatic stabiliser |
| Ser195(141)E(A) | proton acceptor |
| His57(33)E(A) | proton donor |
| Ser195(141)E(A) | nucleofuge |
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