| Name | Peptidase family G5 (prenyl protease 2 family) |
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| Family type peptidase | G05.001 - RCE1 peptidase (Saccharomyces cerevisiae-type) (Saccharomyces cerevisiae), MEROPS Accession MER0004244 (peptidase unit: 1-315) |
| Content of family | Peptidase family G5 contains specialised endopeptidases that typically cleave a C-terminal tripeptide from an isoprenylated protein. |
| History | It should be noted that peptidases in family M48, prenyl-processing peptidase family I, catalyse a similar reaction to those in family G5. The specificities are overlapping (for example, peptidases from both families process the yeast a-mating factor), but they are not identical (Dolence et al., 2000; Trueblood et al., 2000). The sequence of events in the biosynthesis of the proteins that are processed by the prenyl-processing peptidases is (1) condensation of the thiol of a cysteine residue near the C-terminus with farnesyl pyrophosphate or geranylgeranyl pyrophosphate, (2) cleavage of the peptide bond C-terminal to the modified cysteine and liberation of an intact C-terminal tripeptide, and (3) methylation of the new C-terminal carboxyl group. Steps (1) and (3) are catalysed by non-peptidase enzymes.
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| Catalytic type | Glutamic |
| Active site | Active site residues have been identified from the crystal structure of a microcystinase (G05.004) from the archaean Methanococcus maripaludis as Glu140, Glu141, His173, His227 and Asn231. These are located within a large aqueous cavity with their side chains pointing into the cavity, except for Glu141. Glu140 and His173 ligate a water molecule (Hampton et al., 2018), implying that the enzyme is a glutamic peptidase. Previously, peptidases in family G5 had been considered to be either cysteine (Dolence et al. (2000)) or metallo- peptidases (Pei & Grishin (2001)). Because of the distant sequence relationships within the family, only Glu140, Glu141 and His173 can be aligned with residues in microcystinase MlrA from Sphingomonas and RCE1 from Saccharomyces. Residues Glu156, Glu157, His194, His248 and Cys251 from RCE1 (numbering as in the MEROPS Alignment) were considered to be potential active site residues and mutagenic studies by Plummer et al. (2005) found that Glu156, His194 and His248 are critical for activity, but Cys251 is not. |
| Activities and specificities | The specificity of the prenyl-processing peptidases is usually described as cleavage of the '-CaaX' motif, a representation of the C-terminal tetrapeptide of the substrate protein. This cleavage can alternatively be represented: -Cys(R) Xaa-Xaa-Xbb, in which Cys(R) is cysteine in which the thiol is substituted with a C15 (farnesyl) or C20 (geranylgeranyl) side chain, Xaa is normally a small, aliphatic residue, and Xbb is any amino acid. In vitro assays have been made with N-acetyl-S-farnesyl-L-CysVal-Ile-Met as substrate (Ma et al., 1993). A comparison with the prenyl-processing peptidases of family M48 has been made by Trueblood et al. (2000).
Peptidase homologues from bacteria and archaea are described as "microcystinases", degrading the cyclic heptapeptide hepatotoxin microcystin produced by blue-green algae. Peptidases from family M81 perform a similar function. Microcystinase MlrA from Sphingomonas sp. CBA4 degrades microcystin-RR (Ame et al., 2006). The microcystinases in family G5 are only distantly related to eukaryote proteins in the family. |
| Inhibitors | The microcystinase from Methanococcus maripaludis is unaffected by EDTA, but its structural integrity is destroyed by 1,10-phenanthroline. No zinc is present in the solved tertiary structure (Hampton et al., 2018). Peptidase G05.002 was not affected by EDTA (25 mM), 1,10-phenanthroline (1 mM) or compound E-64 (44 micromolar), but there was inhibition by some compounds that have non-specific thiol-reactivity, notably mercurials (Dolence et al., 2000). N-Boc-S-Farnesyl-L-cysteine aldehyde (2 micromolar) is an inhibitor (Ma et al., 1993) as is the corresponding chloromethane (Chen et al., 1996). The pseudo-peptide analogue of the substrate N-acetyl-S-farnesyl-L-CysVal-Ile-Met is a potent competitive inhibitor of Ki 85 nM (Chen et al., 1996). |
| Molecular structure | The tertiary structure of a microcystinase from the archaean Methanococcus maripaludis has been solved (Manolaridis et al., 2013), and shows a protein with eight transmembrane alpha-helices, with the active site residues encased within a large, conical, aqueous cavity some 10 Angstroms within the membrane. |
| Clan | unassigned |
| Biological functions | Proteins that require processing by the prenyl peptidases include fungal mating factors, nuclear lamins, Ras and Ras-related GTP-binding proteins (G proteins), the subunits of trimeric G proteins, protein kinases, and at least one viral protein (Zhang & Casey, 1996). |
| Pharmaceutical and biotech relevance | The metabolism of the oncogene products in particular may be of great importance in tumour biology, so there has been considerable interest in the processing peptidases in families M48 and G5. This being the case, it is remarkable that the catalytic type of the peptidases in G5 still remains to be established beyond doubt.
Microcystins are hepatotoxins produced by blue-green algae. Being cyclic and containing non-standard amino acids, microcystins are not degraded by human digestive enzymes. The discovery of enzymes that can degrade them may enable their removal from contaminated drinking water. |
| Statistics for family G5 | Sequences: | 9185 |
| Identifiers: | 11 |
| Identifiers with PDB entries: | 1 |
| Downloadable files |
Sequence library (FastA format) |
| Sequence alignment (FastA format) |
| Phylogenetic tree (Newick format) |
