Gingipain R

 

Gingipains are key virulence factors of Porphyromonas gingivalis. They are cysteine proteinases with a high specificity for Arg-Xaa or Lys-Xaa. These proteins are single polypeptides with two domains that show homology to the caspases. Gingipain R is implicated in tissue inflammation associated with periodontal diseases. Elucidation of a chemical mechanism for the active site of gingipain R may be useful in design of drugs in the fight against peridontal diseases.

 

Reference Protein and Structure

Sequence
P95493 UniProt (3.4.22.37) IPR012600 (Sequence Homologues) (PDB Homologues)
Biological species
Porphyromonas gingivalis W83 (Bacteria) Uniprot
PDB
1cvr - Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB) (2.0 Å) PDBe PDBsum 1cvr
Catalytic CATH Domains
3.40.50.1460 CATHdb (see all for 1cvr)
Click To Show Structure

Enzyme Reaction (EC:3.4.22.37)

water
CHEBI:15377ChEBI
+
dipeptide
CHEBI:46761ChEBI
→
L-alpha-amino acid
CHEBI:15705ChEBI
Alternative enzyme names: Arg-gingipain, Arg-gingivain-55 proteinase, Arg-gingivain-70 proteinase, Arg-gingivain-75 proteinase, RGP, RGP-1, Argingipain, Arginine-specific cysteine protease, Arginine-specific gingipain, Arginine-specific gingivain, Gingipain-1,

Enzyme Mechanism

Introduction

Cys437 acts as a nucleophile to attack the carbonyl carbon of the peptide bond, forming a tetrahedral intermediate stabilised by an oxyanion hole formed by the backbone amide groups of Cys437 and Gly441. His440 then protonates the leaving group, with Glu381 acting to facilitate this. Activation of water by His440 then occurs to allow hydrolysis of the thiol intermediate.

Catalytic Residues Roles

UniProt PDB* (1cvr)
Gly441 (main-N) Gly212A (main-N) Forms part of the oxyanion hole to stabilise the carbonyl oxygen of the tetrahedral intermediate. electrostatic stabiliser
Cys473 (main-N) Cys244A (main-N) The main-chain nitrogen is involved in formation of the oxyanion hole to stabilise the carbonyl oxygen in the tetrahedral intermediate. electrostatic stabiliser
His440 His211A Protonates leaving group N-terminal amide nitrogen to facilitate collapse of tetrahedral intermediate. Activates water to allow hydrolysis of thiol enzyme intermediate. proton acceptor, proton donor
Cys473 Cys244A The s-gamma atom makes a nucleophilic attack on the carbonyl carbon of the peptide bond, forming a covalent intermediate. nucleofuge, nucleophile, proton acceptor, proton donor
Glu381 Glu152A Facilitates transfer of a proton from His440 to the Xaa leaving group N-terminal nitrogen. electrostatic stabiliser
*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, unimolecular elimination by the conjugate base, intermediate collapse, overall product formed, native state of enzyme regenerated

References

  1. Eichinger A et al. (1999), EMBO J, 18, 5453-5462. Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with a caspase-like fold. DOI:10.1093/emboj/18.20.5453. PMID:10523290.

Step 1. His440 deprotonates Cys473 which activates it so that it can attack the carbon of the carbonyl in a nucleophilic addition which produces the oxyanion intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly212A (main-N) electrostatic stabiliser
Glu152A electrostatic stabiliser
Cys244A (main-N) electrostatic stabiliser
His211A proton acceptor
Cys244A proton donor, nucleophile

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used

Step 2. The oxyanion initiates an elimination resulting in the cleavage of the peptide bond. The amino group of the N-terminal product accepts a proton from His440 and this prevents reformation of the peptide bond.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu152A electrostatic stabiliser
Gly212A (main-N) electrostatic stabiliser
Cys244A (main-N) electrostatic stabiliser
His211A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, overall product formed

Step 3. His440 deprotonates a water, activating the water so that it can attack the carbon of the thioester bond in a nucleophilic addition.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu152A electrostatic stabiliser
Gly212A (main-N) electrostatic stabiliser
Cys244A (main-N) electrostatic stabiliser
His211A proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used

Step 4. The oxyanion initiates another elimination which results in the cleavage of the thioester bond. The released Cys437 now accepts an electron from His440 which returns the enzyme to its native state.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu152A electrostatic stabiliser
Gly212A (main-N) electrostatic stabiliser
Cys244A (main-N) electrostatic stabiliser
His211A proton donor
Cys244A nucleofuge, proton acceptor

Chemical Components

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

Step 1. His440 deprotonates Cys473 which activates it so that it can attack the carbon of the carbonyl in a nucleophilic addition which produces the oxyanion intermediate.

Step 2. The oxyanion initiates an elimination resulting in the cleavage of the peptide bond. The amino group of the N-terminal product accepts a proton from His440 and this prevents reformation of the peptide bond.

Step 3. His440 deprotonates a water, activating the water so that it can attack the carbon of the thioester bond in a nucleophilic addition.

Step 4. The oxyanion initiates another elimination which results in the cleavage of the thioester bond. The released Cys437 now accepts an electron from His440 which returns the enzyme to its native state.

Products.

Contributors

James Torrance, Gemma L. Holliday, Charity Hornby