9.B.149 The M50 Peptidase (M50-P) Family

The M50 Peptidase (S2P-M50) family includes proteins frequently of 700-800 aas in length with six N-terminal or centrally located TMSs. However, other members of the family are relatively small (300-400 aas).  They are integral membrane zinc metaloprotease that cleave transmembrane domains in proteins. They are frequently encoded in gene clusters with lantibiotic biosynthetic enzymes and ABC transporters. For example, Streptomyces griseus encodes in the following order: an ABC-2 type transporter, an ABC-type ATPase (see TC#3.A.1.105.11), a S2P-M50 peptidase with a CBS domain (see 9.B.149.1.1), a lantibiotic synthesis protein and a lantibiotic dehydratase. Other M50 peptidases include Membrane Fusion Protein (MFP; TC# 8.A.1) domains or may have an MFP encoded in the same operon. Still others include ABC-type ATPase domains fused to them, indicating a close relationship with the transporter. Peptidase processing of bacteriocins is known in some cases to occur during transport, and the peptidase and transporter presumably form a complex in the membrane. Many bacteriocin-producing Gram-positive bacteria have ABC exporters that function with an essential MFP (Harley et al. 2000). 



Akiyama, Y., K. Kanehara, and K. Ito. (2004). RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences. EMBO. J. 23: 4434-4442.

Alba, B.M., J.A. Leeds, C. Onufryk, C.Z. Lu, and C.A. Gross. (2002). DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma(E)-dependent extracytoplasmic stress response. Genes Dev. 16: 2156-2168.

Flores, S.K., Y. Deng, Z. Cheng, X. Zhang, S. Tao, A. Saliba, I. Chu, N. Burnichon, A.P. Gimenez-Roqueplo, E. Wang, R.C.T. Aguiar, and P.L.M. Dahia. (2020). Functional Characterization of TMEM127 Variants Reveals Novel Insights into Its Membrane Topology and Trafficking. J Clin Endocrinol Metab 105:.

Harley, K.T., G.M. Djordjevic, T.T. Tseng, and M.H. Saier. (2000). Membrane-fusion protein homologues in gram-positive bacteria. Mol. Microbiol. 36: 516-517.

Kanehara, K., K. Ito, and Y. Akiyama. (2002). YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA. Genes Dev. 16: 2147-2155.

Koide, K., K. Ito, and Y. Akiyama. (2008). Substrate recognition and binding by RseP, an Escherichia coli intramembrane protease. J. Biol. Chem. 283: 9562-9570.

Yokoyama, T., T. Niinae, K. Tsumagari, K. Imami, Y. Ishihama, Y. Hizukuri, and Y. Akiyama. (2021). The Escherichia coli S2P intramembrane protease RseP regulates ferric citrate uptake by cleaving the sigma factor regulator FecR. J. Biol. Chem. 100673. [Epub: Ahead of Print]

Yu, Y.T. and L. Kroos. (2000). Evidence that SpoIVFB is a novel type of membrane metalloprotease governing intercompartmental communication during Bacillus subtilis sporulation. J. Bacteriol. 182: 3305-3309.


TC#NameOrganismal TypeExample

Peptidase M50 with CBS domain


M50 peptidase of Streptomyces griseus (B1W279)


Uncharacterized protein of 525 aas and 8 TMSs


Thermoplasma volcanium (Q97BX9)


Putative Zn-dependent protease of 220 aas

Protease of Bdellovibrio bacteriovorus


Sporulation stage IV FB protein, SpoIVFB, 288 aas and 5 TMSs 

SpoIVFB of Bacillus jeotgali


Integral membrane protease, SpoIVFB or BofB, of 288 aas and 5 or 6 TMSs (Yu and Kroos 2000).

SpoIVFB of Bacillus subtilis


Uncharacterized protease-like protein with 755 aas and 9 TMSs in a 6 + 3 TMS arrangement. The protease cleaves transmembrane domains of substrate proteins. The C-terminal hydrophilic domain and the last TMS resemble the N-terminal parts of membrane fusion proteins (TC# 8.A.1).

UP of Gemmata obscuriglobus


Putative integral membrane protein complex consisting of two or more proteins. Three of these proteins, located adjacent to each other, are listed here with a fourth, having a putative cytochrome c biosynthetic function, is listed with TC# 9.B.14.3.10.

Putative protein complex of Gemmataceae bacterium (freshwater metagenome)

MSR49331, protein of 721 aas and 1 N-terminal TMS with a central MFP (HlyD) domain (TC# 8.A.1) and a C-terminal guanine nucleotide binding protein domain (like TC# 8.A.92.1.2). Its gene is adjacent to MSR49332.
MSR49332, protein of 762 aas and 9 TMSs in a 6 + 3 TMS arrangement with hydrophilic N- and C-terminal regions.
MSR49333, uncharacterized protein of 290 aas with one N-terminal TMS.
[MSR49334, putative cytochrome c biogenesis protein with 8 TMSs listed under TC# 9.B.14.3.10.]


Zinc metalo-protease of 383 aas and 6 TMSs

Protease of Amycolatopsis mediterranei (Nocardia mediterranei)


M50 peptidase with 9 putative TMSs in a 6 + 3 TMS arrangement and a sequence divergent C-terminal Membrane Fusion Protein (MFP) domain.


M50 peptidase of Rhodopirellula baltica (F2AL16)


M50 family peptidase (720aas and 9 TMSs in a 6 + 3 TMS arrangement). This protein may have the M50 peptidase domain at the N-terminus and may have a distant member of the MFP family (8.A.1) as the C-terminal domain. It is encoded within a gene cluster adjacent to a gene coding for a putative phytochrome sensor with a GAF domain in the N-terminal hydrophilic region, followed by 1 or 2 central TMSs, followed by an MFP domain,different from that in the putative peptidase protein (see TC# 8.A.1 for the MFP family) at its C-terminus (631aas; Q3AQQ9). Possibly part of an ABC exporter.


M50 peptidase of Chlorobium chlorochromalii (Q3AQR0)


Uncharacterized protein of 934 aas and 6-7 TMSs

Alveolata (ciliates)

UP of Perkinsus marinus


Uncharacterized protein of 199 aas and 6 TMSs


UP of Methanothermobacter thermautotrophicus


Uncharacterized protein of 373 aas and 8 TMSs


UP of Pyrococcus horikoshii


TC#NameOrganismal TypeExample

Regulator of σW transmembrane metaloprotease, RasP (YluC) of 422 aas and 4 - 6 TMSs. RasP, when defective, causes defects in competence development, protein secretion and membrane protein production (Zweers et al. 2012). σV activation in B. subtilis is controlled by regulated intramembrane proteolysis and requires RasP (Hastie et al. 2013). RasP also cleaves both of the stress response anti-sigma factors, RsiW and RsiV, as well as the cell division protein FtsL, and remnant signal peptides, within their transmembrane segments (Parrell et al. 2017).

RasP of Bacillus subtilis


Membrane metaloprotease of 343 aas and 4-6 TMSs.

Protease of Candidatus Wolfebacteria bacterium


S2P integral membrane protease, RseP (Regulator of sigmaE protease) (YaeL or EcfE), of 450 aas and 5 TMSs in a 3 (N-terminal) + 2 (C-terminal) TMS arrangement (Kanehara et al. 2002; Alba et al. 2002). RseP regulates ferric citrate uptake by cleaving the sigma factor regulator, FecR (Yokoyama et al. 2021). It can also cleave sequences in transmembrane regions of other proteins (such as LacY) as well as liberated signal peptides of beta-lactamase, OmpF, LivK, SecM, PhoA, LivJ, OmpC, Lpp and TorA, probably within the membrane (Akiyama et al. 2004; Koide et al. 2008).

RseP of E. coli