TCID | Name | Domain | Kingdom/Phylum | Protein(s) |
---|---|---|---|---|
1.C.1.1.1 | Colicin Ia. Residues lining the channel have been identified (Kienker et al. 2008). The 3D structure is known (PDB acc # 1CII; Gupta et al. 2023). | Bacteria |
Pseudomonadota | Colicin Ia of E. coli |
1.C.1.1.2 | Colicin Ib | Bacteria |
Pseudomonadota | Colicin Ib of E. coli |
1.C.1.1.3 | Alveicin A (Wertz and Riley, 2004) | Bacteria |
Pseudomonadota | Alveicin A in Hafnia alvei |
1.C.1.1.4 | Alveicin B (Wertz and Riley, 2004) | Bacteria |
Pseudomonadota | Alveicin B in Hafnia alvei |
1.C.1.1.5 | Pore-forming Colicin F(Y) or Colicin FY (Bosák et al. 2012) | Bacteria |
Pseudomonadota | Colicin FY of Yersinia frederiksinii |
1.C.1.1.6 | Pore-forming pyocin S5 of 498 aas, PyoS5. Active against several P. aeruginosa clinical isolates where it causes membrane damage and leakage (Ling et al. 2010). Uses the ferripyochelin (FptA) receptor (Elfarash et al. 2014). A PyoS5 immunity protein prevents cell damage (Rasouliha et al. 2013). | Bacteria |
Pseudomonadota | PyoS5 of Pseudomonas aeruginosa |
1.C.1.2.1 | Colicin K. Similar to Colicin 5 (Pilsl and Braun 1995). | Bacteria |
Pseudomonadota | Colicin K of E. coli |
1.C.1.2.2 | Colicin E1 of 522 aas and 1 C-terminal TMS. Ho et al. (2011) suggested a membrane topological model with a circular arrangement of helices 1-7 in a clockwise direction from the extracellular side and membrane interfacial association of helices 1, 6, 7, and 10 around the central transmembrane hairpin formed by helices 8 and 9. The 3D structure is known (PDB # 2I88; Gupta et al. 2023). ColE1 induces lipid flipping, consistent with the toroidal (proteolipidic) pore model of channel formation (Sobko et al. 2010). The mechanism of channel integration involving the transition of the soluble to membrane-bound form has been presented (Lugo et al. 2016). Colicin E1 uses BtuB as receptor and possibly, the outer membrane TolC protein as the translocator (Cramer et al. 2018). Colicin E1 adopts a closed-channel state at positive transmembrane potentials, correlating with a large tilt angle of alpha-helical TMSs. When the transmembrane potential becomes negative, it inserts into the lipid bilayer with a low tilt angle for the TMSs. Insertion, driven by the negative potential, generates the channel with the open and closed states interconverting reversibly (Su et al. 2019). | Bacteria |
Pseudomonadota | Colicin E1 of E. coli |
1.C.1.2.3 | Colicin 10. Uses the Tsx receptor for uptake (Pilsl and Braun 1995). | Bacteria |
Pseudomonadota | Colicin 10 of E. coli |
1.C.1.2.4 | Cell envelope integrity protein TolA of 459 aa | Bacteria |
Pseudomonadota | TolA of Acinetobacter baumannii |
1.C.1.3.1 | Colicin A. The role of the hydrophobic helical hairpin of the pore-forming domain has been elucidated (Bermejo et al. 2013). Acidic conditions promote membrane insertion (Pulagam and Steinhoff 2013). The 3D structure has been determined (PDB # 1COL | Bacteria |
Pseudomonadota | Colicin A of Citrobacter freundii |
1.C.1.3.2 | Colicin B. Its structural stability and interactions have been studied (Ortega et al. 2001). It is 80% identical to colicin D, and colicin D has a well defined structure (PDB # 1V74; Gupta et al. 2023). | Bacteria |
Pseudomonadota | Colicin B of E. coli |
1.C.1.3.3 | Colicin N (OmpF is the receptor and translocator (Baboolal et al., 2008)). The 3D structure has been determined (PDB# 1A87; Gupta et al. 2023). The 3D structure has been determined (PDB # 1RH7; Gupta et al. 2023). | Bacteria |
Pseudomonadota | Colicin N of E. coli |
1.C.1.3.4 | Colicin S4 (The crystal structure is known (3FEW_X; Arnold et al., 2009)). | Bacteria |
Pseudomonadota | Colicin S4 of E. coli (Q9XB47) |
1.C.1.3.5 | Colicin R of 629 aas and 2 C-terminal TMSs (Rendueles et al. 2014). Colicin U (Cua of 619 aas; O24681) is 94% identical to Colicin R, and Colicin Y (ColY of 629 aas; Q9KJ98) is 90% identical to Colicin R (Smajs et al. 2006). | Bacteria |
Pseudomonadota | Colicin R of E. coli |
1.C.1.3.6 | Colicin-like pore-forming domain protein, PmnH, of 462 aas and 2 C-terminal TMSs. This protein has a dual-toxin architecture, having both an N-terminal colicin M-like domain, potentially interfering with peptidoglycan synthesis, and a colicin N-type domain, a pore-forming module distinct from the colicin Ia-type domain in Pseudomonas aeruginosa pyocin S5 (Ghequire et al. 2017). Enhanced killing activity of PmnH under iron-limited growth conditions is due to parasitism of the ferrichrome-type transporter for entry into target cells, a strategy shown here to be used as well by monodomain colicin M-like bacteriocins from pseudomonads (Ghequire et al. 2017). | Bacteria |
Pseudomonadota | PmnH of Pseudomonas synxantha |
1.C.1.3.7 | Lipid II-degrading bacteriocin PaeM of 289 aas. The 3-d structure is known PDB# (4G75 and 4G76) (Barreteau et al. 2012). | Bacteria |
Pseudomonadota | ColM or PaeM of Pseudomonas aeruginosa |
1.C.1.3.8 | Colicin M of 278 aas. It's 3D structure is known (PDB # 3DA3; Gupta et al. 2023). | Bacteria |
Proteobacterium | Colicin M of E. coli |
1.C.1.4.1 | Colicin E2 or E9 (Mosbahi et al., 2002). Colicin E2 is still in contact with its receptor and import machinery when its nuclease domain enters the cytoplasm (Duche, 2007). Colicin E3 is almost identical to Colicin E3 (RNAase). The crystal structure of Colicin E3 with bound BtuB and with the N-terminal translocation (T) domain of E3 and E9 (DNAase) inserted into the OM OmpF porin has been solved (Cramer et al. 2018) revealing: (I) Details of the initial interaction of the colicin central receptor (R)- and N-terminal T-domain with OM receptors/translocators. (II) Features of the translocon include: (a) high-affinity (K d ≈ 10-9 M) binding of the E3 receptor-binding R-domain E3 to BtuB; (b) insertion of disordered colicin N-terminal domain into the OmpF trimer; (c) binding of the N-terminus, documented for colicin E9, to the TolB protein on the periplasmic side of OmpF. Reinsertion of the colicin N-terminus into the second of the three pores in OmpF implies a colicin anchor site on the periplasmic side of OmpF. (III) Studies on the insertion of nuclease colicins into the cytoplasmic compartment imply that translocation proceeds via the C-terminal catalytic domain, proposed here to insert through the unoccupied third pore of the OmpF trimer, consistent with in vitro occlusion of OmpF channels by the isolated E3 C-terminal domain (Cramer et al. 2018). | Bacteria |
Pseudomonadota | Colicin E9 of E. coli (P09883) Colicin E2 of E. coli (P04419) |
1.C.1.4.2 | Pyocin-S2, Pys2 of 689 aas. Causes breakdown of chromosomal DNA as well as complete inhibition of lipid synthesis in sensitive cells. Prevents biofilm formation in vitro and in vivo (Smith et al. 2012). Binds the FpvA receptor (Elfarash et al. 2012). It forms pores though which the toxin enters the cytoplasm (Parret and De Mot 2000). | Bacteria |
Pseudomonadota | Pvs2 of Pseudomonas aeruginosa |