Family M86

Family

Summary Holotypes Alignment Tree Genomes Structure Literature

Summary for family M86

Family type peptidaseM86.001 - PghP gamma-polyglutamate hydrolase (bacteriophage) (Bacillus phage phiNIT1), MEROPS Accession MER0127162 (peptidase unit: 2-208)
Content of familyPeptidase family M86 contains poly-gamma-glutamyl hydrolases.
History Identifier created: MEROPS 9.6 (29 February 2012)
gamma-PGA hydrolase (PghP; M86.001) was first purified and characterized from bacteriophage phiNIT1 in Bacillus subtilis host cells (Kimura & Itoh, 2003). Inhibition by iodoacetate erroneously led to the conclusion that the enzyme was a cysteine peptidase.
Catalytic typeMetallo
Active site residuesH40 E45 H103 E165 
Active siteThe single catalytic zinc ion is tetrahedrally coordinated by two histidines (His40 and His103), a glutamate (Glu45), and a water molecule. The zinc ligands are conserved and have each been verified by site-directed mutagenesis. From mutagenesis studies, Glu165 is also essential and is probably an active site residue (Fujimoro & Kimura, 2011).
Activities and specificitiesgamma-PGA hydrolase (PghP) can internally hydrolyse gamma-linked poly-DL-glutamic acid (gamma-DL-PGA), giving final products no smaller than trimers, even when subjected to prolonged incubation or the addition of more enzyme (Kimura & Itoh, 2003). PghP poorly hydrolyses gamma-D-PGA, which has a rigid structure and may be unable to fit into the catalytic cleft of the enzyme (Fujimoro & Kimura, 2011).
InhibitorsIodoacetate inhibits the activity of PghP, suggesting it is a thiol-dependent peptidase (Kimura & Itoh, 2003).
Molecular structureThe tertiary structure of PghP has been solved, and shows an open alpha/beta mixed core structure with a seven stranded parallel/antiparallel beta sheet, similar to that of carboxypeptidase A (M14.001) fromf peptidase family M14 (Fujimoro & Kimura, 2011). Because the peptidases have the same topologies for their central beta-sheets, each including a core four-stranded parallel beta-sheet, family M86 is included in clan MC.
ClanMC
Distribution of family Bacteria details  
Archaea details  
Protozoa -  
Fungi -  
Plants details  
Animals -  
Viruses details  
Biological functionsSome B. subtilis strains are able to produce a capsule of gamma-PGA that can function as a physical barrier against bacteriophages. PghP is a phage encoded peptidase and can degrade this barrier, allowing phage progenies to infect encapsulated host cells (Kimura & Itoh, 2003).
Pharmaceutical and biotech relevanceNatto is a Japanese food containing soybeans fermented with B. subtilis. Phage contamination can cause the slime viscosity of natto products to rapidly decrease, reducing their quality. PghP can degrade gamma-PGA capsules (slime) and is hence responsible for the damage to natto products when they are contaminated with phage (Kimura & Itoh, 2003).
Statistics for family M86Sequences:154
Identifiers:1
Identifiers with PDB entries:1
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
PghP gamma-polyglutamate hydrolase (bacteriophage)M86.001Yes
family M86 non-peptidase homologuesnon-peptidase homologue-
family M86 unassigned peptidasesunassigned-