Peptidase C1B, bleomycin hydrolase (IPR004134)
Short name: Peptidase_C1B
Overlapping homologous superfamilies
- Papain-like cysteine peptidase superfamily (IPR038765)
This group of proteins belong to MEROPS peptidase family C1, subfamily C1B. This family contains prokaryotic and eukaryotic aminopeptidases and includes bleomycin hydrolases. Bleomycins are antitumour glycopeptide antibiotics originally isolated from the actinomycete Streptomyces verticillus, and are inactivated by bleomycin hydrolase, which hydrolyses the carboxyamide bond of the beta-aminoalanine moiety [PMID: 4122312]. Other cysteine peptidases from the papain family have no effect on bleomycins [PMID: 8639621, PMID: 2477059]. Bleomycin hydrolase acts mainly as an aminopeptidase on short peptides, but the rat orthologue has been shown to cleave amyloid beta-peptides, acting as an endopeptidase or a carboxypeptidase, as well as an aminopeptidase [PMID: 16472072]. The C terminus is autolytically processed to remove the C-terminal residue [PMID: 9546396]. Bleomycin hydrolase is intracellular and exists naturally as a homohexamer, with all the active site in the central cavity of the barrel [PMID: 7638617]. This molecular organisation prevents native proteins from entering the cavity. The negative C terminus interacts with the positive N terminus of the substrate and anchors it to the active site. The structure of the C terminus resembles that of an inhibitor, such as leupeptin, bound to an active peptidase, such as papain, and the distance of the C terminus from the active site acts as a molecular ruler to confer positional specificity [PMID: 9546396].
A cysteine peptidase is a proteolytic enzyme that hydrolyses a peptide bond using the thiol group of a cysteine residue as a nucleophile. Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. Cysteine peptidases can be grouped into fourteen different clans, with members of each clan possessing a tertiary fold unique to the clan. Four clans of cysteine peptidases share structural similarities with serine and threonine peptidases and asparagine lyases. From sequence similarities, cysteine peptidases can be clustered into over 80 different families [PMID: 11517925]. Clans CF, CM, CN, CO, CP and PD contain only one family.
Cysteine peptidases are often active at acidic pH and are therefore confined to acidic environments, such as the animal lysosome or plant vacuole. Cysteine peptidases can be endopeptidases, aminopeptidases, carboxypeptidases, dipeptidyl-peptidases or omega-peptidases. They are inhibited by thiol chelators such as iodoacetate, iodoacetic acid, N-ethylmaleimide or p-chloromercuribenzoate.
Clan CA includes proteins with a papain-like fold. There is a catalytic triad which occurs in the order: Cys/His/Asn (or Asp). A fourth residue, usually Gln, is important for stabilising the acyl intermediate that forms during catalysis, and this precedes the active site Cys. The fold consists of two subdomains with the active site between them. One subdomain consists of a bundle of helices, with the catalytic Cys at the end of one of them, and the other subdomain is a beta-barrel with the active site His and Asn (or Asp). There are over thirty families in the clan, and tertiary structures have been solved for members of most of these. Peptidases in clan CA are usually sensitive to the small molecule inhibitor E64, which is ineffective against peptidases from other clans of cysteine peptidases [PMID: 7044372].
Clan CD includes proteins with a caspase-like fold. Proteins in the clan have an alpha/beta/alpha sandwich structure. There is a catalytic dyad which occurs in the order His/Cys. The active site His occurs in a His-Gly motif and the active site Cys occurs in an Ala-Cys motif; both motifs are preceded by a block of hydrophobic residues [PMID: 9891971]. Specificity is predominantly directed towards residues that occupy the S1 binding pocket, so that caspases cleave aspartyl bonds, legumains cleave asparaginyl bonds, and gingipains cleave lysyl or arginyl bonds.
Clan CE includes proteins with an adenain-like fold. The fold consists of two subdomains with the active site between them. One domain is a bundle of helices, and the other a beta barrell. The subdomains are in the opposite order to those found in peptidases from clan CA, and this is reflected in the order of active site residues: His/Asn/Gln/Cys. This has prompted speculation that proteins in clans CA and CE are related, and that members of one clan are derived from a circular permutation of the structure of the other.
Clan CL includes proteins with a sortase B-like fold. Peptidases in the clan hydrolyse and transfer bacterial cell wall peptides. The fold shows a closed beta barrel decorated with helices with the active site at one end of the barrel [PMID: 14725770]. The active site consists of a His/Cys catalytic dyad.
Cysteine peptidases with a chymotrypsin-like fold are included in clan PA, which also includes serine peptidases. Cysteine peptidases that are N-terminal nucleophile hydrolases are included in clan PB. Cysteine peptidases with a tertiary structure similar to that of the serine-type aspartyl dipeptidase are included in clan PC. Cysteine peptidases with an intein-like fold are included in clan PD, which also includes asparagine lyases.