Cathepsin S

 

Cathepsin S is a cysteine proteinase of the papain superfamily and is involved in generation of a major histocompatability complex class II restricted T-cell response by antigen-presenting cells. Expression is almost exclusively restricted to cells of lymphoid origin. This enzyme is therefore important for study in reference to immune-related disorders.

 

Reference Protein and Structure

Sequence
P25774 UniProt (3.4.22.27) IPR013128 (Sequence Homologues) (PDB Homologues)
Biological species
Homo sapiens (Human) Uniprot
PDB
1glo - Crystal Structure of Cys25Ser mutant of human cathepsin S (2.2 Å) PDBe PDBsum 1glo
Catalytic CATH Domains
3.90.70.10 CATHdb (see all for 1glo)
Click To Show Structure

Enzyme Reaction (EC:3.4.22.27)

water
CHEBI:15377ChEBI
+
dipeptide
CHEBI:46761ChEBI
→
L-alpha-amino acid
CHEBI:15705ChEBI

Enzyme Mechanism

Introduction

Cathepsin S is a cysteine protease. The resting state contains a thioloate-imidazolium pair (Cys 25 and His 164) that is stabilised by Asn 184. Cys 25 attacks the peptide carbonyl nucleophilically, having been activated by deprotonation by His 164 which is in turn activated to act as a base by Asn 184, to form an acyl enzyme intermediate, with His 164 protonating the departing amine. Negative charge that accumulates on the substrate carbonyl oxygen during the reaction is stabilised by an 'oxyanion-hole' involving the side chain of Gln 19 and the backbone NH of Cys 25. The thioester intermediate is then hydrolysed by a water molecule that is deprotonated by His 164 acting as a general base.

Catalytic Residues Roles

UniProt PDB* (1glo)
His278 His164A Acts as a general acid/base catalyst to activate Cys 25 and a water molecule for nucleophilic attack, and to facilitate loss of the leaving groups by proton donation. proton acceptor, proton donor
Asn298 Asn184A Activates and stabilises His 164 to allow it to act as a general acid/base catalyst. electrostatic stabiliser
Cys139 Ser25A Acts as a nucleophile in the attack of the scissile bond. nucleofuge, nucleophile, proton acceptor, proton donor
Gln133, Cys139 (main-N) Gln19A, Ser25A (main-N) Forms part of the oxyanion hole to stabilise the development of negative charge in the transition state. 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. Turkenburg JP et al. (2002), Acta Crystallogr D Biol Crystallogr, 58, 451-455. Structure of a Cys25→Ser mutant of human cathepsin S. DOI:10.1107/s0907444901021825. PMID:11856830.
  2. Kaulmann G et al. (2006), Protein Sci, 15, 2619-2629. The crystal structure of a Cys25 -> Ala mutant of human procathepsin S elucidates enzyme-prosequence interactions. DOI:10.1110/ps.062401806. PMID:17075137.
  3. Pauly TA et al. (2003), Biochemistry, 42, 3203-3213. Specificity determinants of human cathepsin s revealed by crystal structures of complexes. DOI:10.1021/bi027308i. PMID:12641451.

Step 1. His164 deprotonates Cys25, activating it so that it can nucleophilically attack the carbon of the scissille bond which produces the oxyanion intermediate.

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Catalytic Residues Roles

Residue Roles
Gln19A electrostatic stabiliser
Asn184A electrostatic stabiliser
Ser25A (main-N) electrostatic stabiliser
Ser25A proton donor, nucleophile
His164A proton acceptor

Chemical Components

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

Step 2. The oxyanion initiates an elimantion resulting in the cleavage of the scissille bond. The amino group of the N-terminal product then accepts a proton from His164 which prevents reformation of the peptide bond.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln19A electrostatic stabiliser
Ser25A (main-N) electrostatic stabiliser
Asn184A electrostatic stabiliser
His164A proton donor

Chemical Components

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

Step 3. His164 abstracts a proton from water resulting in the activation of it so that it can go on to attack the carbon of the thioester bond in a nucleophilic addition.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln19A electrostatic stabiliser
Ser25A (main-N) electrostatic stabiliser
Asn184A electrostatic stabiliser
His164A proton acceptor

Chemical Components

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

Step 4. The oxyanion initiates another elimination resulting in the cleavage of the thioester bond. The released Cys25 can now accept a proton from His164 resulting in the regeneration of the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln19A electrostatic stabiliser
Ser25A (main-N) electrostatic stabiliser
Asn184A electrostatic stabiliser
Ser25A nucleofuge
His164A proton donor
Ser25A 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. His164 deprotonates Cys25, activating it so that it can nucleophilically attack the carbon of the scissille bond which produces the oxyanion intermediate.

Step 2. The oxyanion initiates an elimantion resulting in the cleavage of the scissille bond. The amino group of the N-terminal product then accepts a proton from His164 which prevents reformation of the peptide bond.

Step 3. His164 abstracts a proton from water resulting in the activation of it so that it can go on to attack the carbon of the thioester bond in a nucleophilic addition.

Step 4. The oxyanion initiates another elimination resulting in the cleavage of the thioester bond. The released Cys25 can now accept a proton from His164 resulting in the regeneration of the native state of the enzyme.

Products.

Contributors

Gary McDowell, Gemma L. Holliday, Charity Hornby