Family S55


Summary Holotypes Alignment Tree Genomes Literature

Summary for family S55

NamePeptidase family S55 (SpoIVB peptidase family)
Family type peptidaseS55.001 - SpoIVB peptidase (Bacillus subtilis), MEROPS Accession MER0003459 (peptidase unit: 188-426)
Content of familyFamily S55 contains endopeptidases.
History Identifier created: MEROPS 5.7 (17 December 2001)
Sporulation in Bacillus has been divided into stages numbered I-VII, and the stage number is included in the name of any gene that is active at that particular stage. During stage II, the precursor of the spore (the prespore) develops and is separated from the mother cell by a septum; both mother cell and prespore each have a complete genome. During stage III the prespore becomes a forespore when the chromosome is surrounded by inner and outer membranes. Stage IV is characterized by cortex formation in which a multi-layered peptidoglucan forms between these inner and outer membranes. Sporulation is controlled by a number of σ transcription factors, principally σE, σF, σG and σK. Proteolytic processing of the precursors of σ factors occurs during stages II and IV; SpoIVB is part of a cascade that leads to the activation of pro-σK. Other families of peptidases involved in aspects of spore production are M50, A36 and U57.
Catalytic typeSerine
Active site residuesH236 D363 S378 
Active siteThe active site residues have been identified by site directed mutagenesis (Hoa et al., 2002). In addition, Asp149 is also a critical residue for associating with substrates (Hoa et al., 2001). This lies within the PDZ domain and not within the peptidase unit.
Activities and specificitiesThe only known cleavages are at autoprocessing sites that activate the precursor by releasing a propeptide. However, no cleavage consensus is apparent. Cleavage sites within the substrates SpoIVFA and BofA have not been precisely determined, but SpoIVFA is known to be cleaved within the C-terminal domain between residues 145 and 175 (Dong & Cutting, 2003).
Molecular structureThe tertiary structure has not been determined. From the primary structure, there is an N-terminal hydrophobic peptide which has been described as 'prolipoprotein-like' and helps the protein associate and perhaps cross the inner forespore membrane. The mature protein has a PDZ domain towards the N-terminus which is believed to be important for associating the peptidase with its substrates, including self-association with the precursor (Hoa & Cutting, 2004). The peptidase unit is the C-terminal two-thirds of the mature protein. From the order of the catalytic residues and the nature of the motifs around them (see the Alignment), the fold for members of the family is predicted to be similar to that of chymotrypsin (S01.001) and family S55 is included in clan PA.
Basis of clan assignmentPredicted active site residues for members of this family and family S1 occur in the same order in the sequence: H, D, S.
Distribution of family Bacteria details  
Archaea -  
Protozoa -  
Fungi -  
Plants -  
Animals -  
Viruses -  
Biological functionsThe proIVB gene is expressed only in the forespore and is under the control of two σ factors: EσF and EσG. Activity of SpoIVB is modulated by the BofC protein, probably via interaction with the PDZ domain (Gomez & Cutting, 1996). Pro-σK is synthesized in the mother cell chamber, and for SpoIVB to have its effect, the precursor has to be secreted across the inner forespore membrane. It is thought that the N-terminal lipoprotein-like leader sequence facilitates secretion, accompanied by unfolding during which cleavage occurs in trans, releasing SpoIVB from the membrane. SpoIVB does not itself activate pro-σK, but instead activates SpoIVFB, which is the peptidase that does. SpoIVFB is a zinc metallopeptidase (M50.002) which is part of a complex embedded in the outer membrane of the forespore. The other components of this complex are SpoIVFA and BofA, both of which are inhibitors of SpoIVFB and have their C-terminal domains between the inner and outer forespore membranes. SpoIVB binds to BofA via the PDZ domain and is then able to cleave SpoIVFA and at the C-terminus (Dong & Cutting, 2004), which in turn leads to the activation of SpoIVFB and cleavage of pro-σK (Hoa & Cutting, 2004). The activation of pro-σK is known as the σK checkpoint, and is essential for the proper development of spores (Dong & Cutting, 2004).
Statistics for family S55Sequences:334
Identifiers with PDB entries:0
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
SpoIVB peptidaseS55.001-
hypothetical protein Acid345_3562non-peptidase homologue-
family S55 unassigned peptidasesunassigned-