|Name||Peptidase family S49 (protease IV family)|
|Family type peptidase||S49.001 - signal peptide peptidase A (Escherichia coli), MEROPS Accession MER0001299 (peptidase unit: 46-618)|
|Content of family||Peptidase family S49 contains endopeptidases.|
Identifier created: MEROPS 5.00 (20 April 2000)|
Signal peptide peptidase A (SppA, S49.001, originally named protease IV) was probably discovered by Pacaud in E. coli (Pacaud, 1982; Pacaud, 1982), although the size of 34 kDa reported by Pacaud is only about half that currently accepted. Signal peptide peptidase A is so termed because it can degrade the released signal peptide of a lipoprotein. There are unrelated functional signal peptide peptidases including oligopeptidase A (M03.004) in bacteria and impas 1 endopeptidase (A22.003) in eukaryotes. There is also an unrelated "protease IV" in Pseudomonas aeruginosa (S01.281).
Many of the prokaryotic homologues are annotated as similar to the NfeD protein in the sequence databases. However, this is an error, because the original NfeD protein was a cyclodeaminase that shows no homology to the proteins in family S49 (Green et al., 2004). Green et al propose that these proteins instead be termed STOPP proteins, for Stomatin Operon Partner Protein.
|Active site||From the tertiary structure of SppA from Escherichia coli a catalytic triad has been proposed consisting of Lys209, Ser409 and Ser432 in which Lys209 is the general base, the hydroxyl group of Ser409 is the nucleophile and Ser432 orientates the lysine (Kim et al., 2009). The active site Lys is in the N-terminal domain and the active site serines in the C-terminal domain. In protein C from bacteriophage lambda (S49.003), which consists of only one domain, the active site residues are in the order Ser166, Ser188 and Lys218 (Medina et al., 2010).|
|Activities and specificities||SppA is most active at pH 7.2 - 7.6. It hydrolyzes the N-blocked p-nitrophenyl esters of Gly, Ala, Phe, Val, Leu and (more slowly) Trp; Z-Val-NHPhNO2 has been used as an assay substrate (Pacaud, 1982; Ichihara et al., 1984). SppA does not hydrolyze casein, but is reported to hydrolyze some of the proteins present in a detergent extract of bacterial membranes (Pacaud, 1982; Palmer & St. John, 1987). Analysis of the peptide products of the SppA-catalyzed hydrolysis of the 20-amino acid lipoprotein signal peptide suggests that it does not require a free N- or C-terminus. It prefers hydrophobic amino acids on either side of the scissile bond and will not cleave a peptide containing fewer than six amino acids.|
|Inhibitors||SppA from E. coli is inhibited by DFP, PMSF, antipain, leupeptin, chymostatin and elastatinal, but not by p-aminobenzamidine, EDTA, pCMB, iodoacetate, TLCK or 2-mercaptoethanol (Pacaud, 1982; Ichihara et al., 1984).|
|Molecular structure||The tertiary structure of SppA from Escherichia coli has been determined (Kim et al., 2009). The structure shows that the N- and C-terminal domains are structurally related probably derived from an ancestral gene duplication and fusion event. The structure is similar to that of endopeptidase clp from family S14, the active site residues can be superimposed and both families are included in the same clan, SK. Unlike endopeptidase clp, the proteins of family S49 contain multiple membrane-spanning domains (Green et al., 2004). In work with recombinant SppA from E. coli it was shown that the 67-kDa monomers could associate into tetramers in solution. Protein C from bacteriophage lambda consists of a single domain (Medina et al., 2010).|
|Basis of clan assignment||Predicted active site serine for members of this family and family S14 occur in the same order in the sequence: S, R/H, D.|