1.B.6 The OmpA-OmpF Porin (OOP) Family

The large OOP family includes the functionally well characterized OmpA porin of E. coli as well as the OmpF (OprF) porin of Pseudomonas aeruginosa (Baldermann et al., 1998). Both proteins contain an N-terminal 8 β-strand transmembrane domain and a cell surface C-terminal peptidoglycan-interaction domain (Grizot and Buchanan, 2004). Only this latter domain exhibits extensive sequence similarity with E. coli OmpA and M. tuberculosis OmpATb. OmpATb has been reported to be a low activity channel that is essential for adaptation of M. tuberculosis to low pH and survival in mouse macrophage, but channel activity has been questioned (Niederweis, 2003).OmpA proteins and their many homologues probably all form structures consisting of eight transmembrane, all next neighbor, antiparallel, amphipathic β-strands. They form small β-barrels with short turns at the periplasmic barrel ends, and long flexible loops at the external ends. A 1.65 Å resolution monomeric structure is available for the E. coli OmpA porin (Pautsch and Schulz, 2000). A tetrameric quarternary structure has been proposed in which the subunits of the tetramer dissociate relatively readily. However, monomeric structures are proposed for other members of this family (Gribun et al., 2004).

The OmpA family consists of heat-modifiable, surface-exposed, porin proteins that are in high-copy number in the outer membranes of many Gram-negative bacteria. OmpA proteins generally have  an N-terminal, eight-stranded, anti-parallel β barrel embedded in the outer membrane while the C-terminal domain is globular and located in the periplasmic space. Escherichia coli OmpA is the best characterized of the proteins, but homologues from pathogenic bacteria include Pseudomonas aeruginosa OprF, Haemophilus influenzae P5, Klebsiella pneumoniae OmpA, and Chlamydia trachomatis major outer membrane protein (MOMP). OmpA from the veterinary pathogens Mannheimia haemolytica, Haemophilus parasuis, Leptospira interrogans, and Pasteurella multocida have been studied to a lesser extent (Confer and Ayalew 2013). Among many of the pathogenic bacteria, OmpA proteins have important pathogenic roles including bacterial adhesion, invasion, or intracellular survival as well as evasion of host defenses or stimulators of pro-inflammatory cytokine production. These pathogenic roles are most commonly associated with central nervous system, respiratory and urogenital diseases. Additionally, OmpA family proteins can serve as targets of the immune system with immunogenicity related to surface-exposed loops of the molecule. In several cases, OmpA proteins are under evaluation as potential vaccine candidates (Confer and Ayalew 2013).

The P. aeruginosa OmpF (1.B.6.1.2) exists in two conformations: a minority single domain conformer and a majority two domain conformer (Sugawara et al., 2006). Only the former inserts into liposomes to give high conductance channel activity (Nestorovich et al., 2006). The active conformation is present only for short times (Nestorovich et al., 2006) accounting for low permeability reported previously.

The OOP family proteins may exhibit structural similarity with well-characterized virulence proteins such as the neisserial opacity (Opa) adhesins, the Salmonella Rck complement resistance protein, the Salmonella PagC intramacrophage survival protein, and the Yersinia Ail attachment/invasion protein (Baldermann et al., 1998). However, sequence similarity with these proteins is insufficient to establish homology. These protein β-barrels resemble those of the lipocalin family although the members of these two protein families serve entirely different functions and show no observable sequence similarity. OmpA of E. coli is required for bacterial conjugation and for maintenance of outer membrane stability.

Tachikawa and Kato 2011 isolated temperature-sensitive mutants of the E. coli bamD gene, which is essential for the assembly of β-barrel outer membrane proteins. As their multicopy suppressor, they identified a novel yiaD gene encoding a putative lipoprotein, YiaD with 3 putative N-terminal TMSs and a C-terminal peptidoglycan-binding domain (see 1.B.6.13.1). Mutations of its OmpA domain, which is required for interaction with peptidoglycan, affected suppression, suggesting that interaction with peptidoglycan is important for YiaD function.  These proteins show extensive sequence similarity with other members of TC families 1.B.6 as well as members of family 9.B.153, and are homologous to them in these regions.  Since family 1.B.6 members are members of the TC Outer Membrane Pore-forming Protein (OMPPI) Superfamily I, families 9.B.153 and 9.B.170, are probably also member of this superfamily. However, if this is just an OmpA-like peptidoglycan binding-domain, these families may not be bonefide members of this superfamily throughout their lengths.

Members of the Ail/Lom family of outer membrane proteins, which are homologous to OmpA of E. coli (1.B.6.1.2), provide protection from complement-dependent killing for a number of pathogenic bacteria. The Y. pestis KIM genome encodes four Ail/Lom family proteins. The Ail (Attachment inversion locus; 182aas) protein is essential for Y. pestis to resist complement-mediated killing. High-level expression of the three other Y. pestis Ail/Lom family proteins (the y1682, y2034, and y2446 proteins) provided no protection against complement-mediated bacterial killing (Bartra et al., 2008).

Intragenic duplication of the 8-stranded OmpX β-barrel produces a functional pore (Omp2X) the size of the OmpC porin (1.B.1.1.3) channel, a natural 16 stranded β-barrel (Arnold et al. 2007).  This provides a potential mechanism for generating larger porins of 16 TMSs from smaller porins of 8 TMSs.


This family belongs to the Outer Membrane Pore-forming Protein I (OMPP-I) Superfamily .
 

References:

Arnold, T., M. Poynor, S. Nussberger, A.N. Lupas, and D. Linke. (2007). Gene duplication of the eight-stranded β-barrel OmpX produces a functional pore: a scenario for the evolution of transmembrane β-barrels. J. Mol. Biol. 366: 1174-1184.
Arora, A., D. Rinehart, G. Szabo, and L.K. Tamm. (2000). Refolded outer membrane protein A of Escherichia coli forms ion channels with two conductance states in planar lipid bilayers. J. Biol. Chem. 275: 1594-1600.
Baldermann, C., A. Lupas, J. Lubieniecki, and H. Engelhardt. (1998). The regulated outer membrane protein Omp21 from Comamonas acidovorans is identified as a member of a new family of eight-stranded β-sheet proteins by its sequence and properties. J. Bacteriol. 180: 3741-3749.
Bartra, S.S., K.L. Styer, D.M. O'Bryant, M.L. Nilles, B.J. Hinnebusch, A. Aballay, and G.V. Plano. (2008). Resistance of Yersinia pestis to complement-dependent killing is mediated by the Ail outer membrane protein. Infect. Immun. 76: 612-622.
Brinkman, F.S., M. Bains, and R.E.W. Hancock. (2000). The amino terminus of Pseudomonas aeruginosa outer membrane protein OprF forms channels in lipid bilayer membranes: correlation with a three-dimensional model. J. Bacteriol. 182: 5251-5255.
Brosig, A., J. Nesper, W. Boos, W. Welte, and K. Diederichs. (2009). Crystal structure of a major outer membrane protein from Thermus thermophilus HB27. J. Mol. Biol. 385: 1445-1455.
Cassin, E.K. and B.S. Tseng. (2019). Pushing beyond the envelope: the potential roles of OprF in biofilm formation and pathogenicity. J. Bacteriol. [Epub: Ahead of Print]
Chevalier, G., H. Duclohier, D. Thomas, E. Shechter, and H. Wróblewski. (1993). Purification and characterization of protein H, the major porin of Pasteurella multocida. J. Bacteriol. 175: 266-276.
Choi, C.H., E.Y. Lee, Y.C. Lee, T.I. Park, H.J. Kim, S.H. Hyun, S.A. Kim, S.K. Lee, and J.C. Lee. (2005). Outer membrane protein 38 of Acinetobacter baumannii localizes to the mitochondria and induces apoptosis of epithelial cells. Cell Microbiol 7: 1127-1138.
Confer, A.W. and S. Ayalew. (2013). The OmpA family of proteins: roles in bacterial pathogenesis and immunity. Vet Microbiol 163: 207-222.
Dabo, S.M., A. Confer, M. Montelongo, P. York, and J.H. Wyckoff, 3rd. (2008). Vaccination with Pasteurella multocida recombinant OmpA induces strong but non-protective and deleterious Th2-type immune response in mice. Vaccine 26: 4345-4351.
Dupont, M., E. Dé, R. Chollet, J. Chevalier, and J.M. Pagès. (2004). Enterobacter aerogenes OmpX, a cation-selective channel mar- and osmo-regulated. FEBS Lett. 569: 27-30.
Estrada Mallarino, L., E. Fan, M. Odermatt, M. Müller, M. Lin, J. Liang, M. Heinzelmann, F. Fritsche, H.J. Apell, and W. Welte. (2015). TtOmp85, a β-Barrel Assembly Protein, Functions by Barrel Augmentation. Biochemistry 54: 844-852.
Fernández, C., C. Hilty, G. Wider, P. Güntert, and K. Wüthrich. (2004). NMR structure of the integral membrane protein OmpX. J. Mol. Biol. 336: 1211-1221.
Gao, T., L. Ju, J. Yin, and H. Gao. (2015). Positive regulation of the Shewanella oneidensis OmpS38, a major porin facilitating anaerobic respiration, by Crp and Fur. Sci Rep 5: 14263.
Giacani, L., S.L. Brandt, W. Ke, T.B. Reid, B.J. Molini, S. Iverson-Cabral, G. Ciccarese, F. Drago, S.A. Lukehart, and A. Centurion-Lara. (2015). Transcription of TP0126, Treponema pallidum putative OmpW homolog, is regulated by the length of a homopolymeric guanosine repeat. Infect. Immun. 83: 2275-2289.
Gribun, A., D.J. Katcoff, G. Hershkovits, I. Pechatnikov, and Y. Nitzan. (2004). Cloning and characterization of the gene encoding for OMP-PD porin: the major Photobacterium damsela outer membrane protein. Curr. Microbiol. 48: 167-174.
Gribun, A., Y. Nitzan, I. Pechatnikov, G. Hershkovits, and D.J. Katcoff. (2003). Molecular and structural characterization of the HMP-AB gene encoding a pore-forming protein from a clinical isolate of Actinetobacter baumannii. Curr. Microbiol. 47: 434-443.
Grizot, S. and S.K. Buchanan. (2004). Structure of the OmpA-like domain of RmpM from Neisseria meningitidis. Mol. Microbiol. 51: 1027-1037.
Hancock, R.E.W. and F.S.L. Brinkman. (2002). Function of Pseudomonas porins in uptake and efflux. Annu. Rev. Microbiol. 56: 17-38.
Hölzer, M., C. Reuschel, F. Vorimore, K. Laroucau, and K. Sachse. (2025). Exploring the genomic landscape of Chlamydiifrater species: novel features include multiple truncated major outer membrane proteins, unique genes and chlamydial plasticity zone orthologs. Access Microbiol 7:.
Hou, V.C., G.R. Moe, Z. Raad, T. Wuorimaa, and D.M. Granoff. (2003). Conformational epitopes recognized by protective anti-neisserial surface protein A antibodies. Infect. Immun. 71: 6844-6849.
Iida, A., Y. Ohnishi, and S. Horinouchi. (2008). An OmpA family protein, a target of the GinI/GinR quorum-sensing system in Gluconacetobacter intermedius, controls acetic acid fermentation. J. Bacteriol. 190: 5009-5019.
Iyer, R., S.H. Moussa, T.F. Durand-Réville, R. Tommasi, and A. Miller. (2018). Acinetobacter baumannii OmpA Is a Selective Antibiotic Permeant Porin. ACS Infect Dis 4: 373-381.
Jeanteur, D., J.H. Lakey, and F. Pattus. (1991). The bacterial porin superfamily: sequence alignment and structure prediction. Mol. Microbiol. 5: 2153-2164.
Jeanteur, D., J.H. Lakey, and F. Pattus. (1994). The porin superfamily: diversity and common features. In: Bacterial Cell Wall (Ghuysen, J.M. and R. Hakenbeck,eds.). Elsevier, Amsterdam, pp. 363-380.
Jyothisri, K., V. Deepak, and M.R. Rajeswari. (1999). Purification and characterization of a major 40 kDa outer membrane protein of Acinetobacter baumannii. FEBS Lett. 443: 57-60.
Khalid, S., P.J. Bond, T. Carpenter, and M.S. Sansom. (2008). OmpA: gating and dynamics via molecular dynamics simulations. Biochim. Biophys. Acta. 1778: 1871-1880.
Kleinschmidt, J.H. (2006). Folding kinetics of the outer membrane proteins OmpA and FomA into phospholipid bilayers. Chem Phys Lipids 141: 30-47.
Kleinschmidt, J.H. and L.K. Tamm. (1996). Folding intermediates of a β-barrel membrane protein. Kinetic evidence for a multi-step membrane insertion mechanism. Biochemistry 35: 12993-13000.
Liu, C., R. Mesman, A. Pol, F. Angius, and H.J.M. Op den Camp. (2023). Identification and characterisation of a major outer membrane protein from Methylacidiphilum fumariolicum SolV. Antonie Van Leeuwenhoek 116: 1227-1245.
Maccarini, M., L. Gayet, J.P. Alcaraz, L. Liguori, B. Stidder, E.B. Watkins, J.L. Lenormand, and D.K. Martin. (2017). Functional Characterization of Cell-Free Expressed OprF Porin from Pseudomonas aeruginosa Stably Incorporated in Tethered Lipid Bilayers. Langmuir 33: 9988-9996.
Mahalakshmi R. and Marassi FM. (2008). Orientation of the Escherichia coli outer membrane protein OmpX in phospholipid bilayer membranes determined by solid-State NMR. Biochemistry. 47(25):6531-8.
Mahalakshmi, R., C.M. Franzin, J. Choi, and F.M. Marassi. (2007). NMR structural studies of the bacterial outer membrane protein OmpX in oriented lipid bilayer membranes. Biochim. Biophys. Acta. 1768: 3216-3224.
Marassi, F.M. (2011). Mycobacterium tuberculosis Rv0899 defines a family of membrane proteins widespread in nitrogen-fixing bacteria. Proteins 79: 2946-2955.
Mishra M., Ressler A., Schlesinger LS. and Wozniak DJ. (2015). Identification of OprF as a Complement Component C3 Binding Acceptor Molecule on the Surface of Pseudomonas aeruginosa. Infect Immun. 83(8):3006-14.
Molle, V., N. Saint, S. Campagna, L. Kremer, E. Lea, P. Draper, and G. Molle. (2006). pH-dependent pore-forming activity of OmpATb from Mycobacterium tuberculosis and characterization of the channel by peptidic dissection. Mol. Microbiol. 61: 826-837.
Nestorovich, E.M., E. Sugawara, H. Nikaido, and S.M. Bezrukov. (2006). Pseudomonas aeruginosa porin OprF: properties of the channel. J. Biol. Chem. 281: 16230-16237.
Niederweis, M. (2003). Mycobacterial porins – new channel proteins in unique outer membranes. Mol. Microbiol. 49: 1167-1177.
Nikaido, H. (1992). Porins and specific channels of bacterial outer membranes. Mol. Microbiol. 6: 435-442.
Pautsch, A. and G.E. Schulz. (2000). High-resolution structure of the OmpA membrane domain. J. Mol. Biol. 298: 273-282.
Poppleton, D.I., M. Duchateau, V. Hourdel, M. Matondo, J. Flechsler, A. Klingl, C. Beloin, and S. Gribaldo. (2017). Outer Membrane Proteome of A Diderm Firmicute of the Human Microbiome. Front Microbiol 8: 1215.
Raterman, E.L., D.D. Shapiro, D.J. Stevens, K.J. Schwartz, and R.A. Welch. (2013). Genetic analysis of the role of yfiR in the ability of Escherichia coli CFT073 to control cellular cyclic dimeric GMP levels and to persist in the urinary tract. Infect. Immun. 81: 3089-3098.
Raynaud, C., K.G. Papavinasasundaram, R.A. Speight, B. Springer, P. Sander, E.C. Böttger, M.J. Colston, and P. Draper. (2002). The functions of OmpATb, a pore-forming protein of Mycobacterium tuberculosis. Mol. Microbiol. 46: 191-201.
Renault, M., O. Saurel, J. Czaplicki, P. Demange, V. Gervais, F. Löhr, V. Réat, M. Piotto, and A. Milon. (2009). Solution state NMR structure and dynamics of KpOmpA, a 210 residue transmembrane domain possessing a high potential for immunological applications. J. Mol. Biol. 385: 117-130.
Renault, M., O. Saurel, P. Demange, V. Reat, and A. Milon. (2010). Solution-state NMR spectroscopy of membrane proteins in detergent micelles: structure of the Klebsiella pneumoniae outer membrane protein A, KpOmpA. Methods Mol Biol 654: 321-339.
Saint, N., C. El Hamel, E. Dé, and G. Molle. (2000). Ion channel formation by N-terminal domain: a common feature of OprFs of Pseudomonas and OmpA of Escherichia coli. FEMS Microbiol. Lett. 190: 261-265.
Schulz, G.E. (1996). Porins: general to specific, native to engineered passive pores. Curr. Opin. Struc. Biol. 6: 485-490.
Scribano, D., E. Cheri, A. Pompilio, G. Di Bonaventura, M. Belli, M. Cristina, L. Sansone, C. Zagaglia, M. Sarshar, A.T. Palamara, and C. Ambrosi. (2024). Acinetobacter baumannii OmpA-like porins: functional characterization of bacterial physiology, antibiotic-resistance, and virulence. Commun Biol 7: 948.
Senaratne, R.H., J. Mobasheri, K.G. Papavinasasundaram, P. Jenner, E.D.A. Lea, and P. Draper. (1998). Expression of a gene for a porin-like protein of the OmpA family from Mycobacterium tuberculosis H37Rv. J. Bacteriol. 180: 3541-3547.
Song, H., J. Huff, K. Janik, K. Walter, C. Keller, S. Ehlers, S.H. Bossmann, and M. Niederweis. (2011). Expression of the ompATb operon accelerates ammonia secretion and adaptation of Mycobacterium tuberculosis to acidic environments. Mol. Microbiol. 80: 900-918.
Stancik, L.M., D.M. Stancik, B. Schmidt, D.M. Barnhart, Y.N. Yoncheva, and J.L. Slonczewski. (2002). pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J. Bacteriol. 184: 4246-4258.
Sugawara, E. and H. Nikaido. (1992). Pore-forming activity of OmpA protein of Escherichia coli. J. Biol. Chem. 267: 2507-2511.
Sugawara, E. and H. Nikaido. (1994). OmpA protein of Escherichia coli outer membrane occurs in open and closed channel forms. J. Biol. Chem. 269: 17981-17987.
Sugawara, E. and H. Nikaido. (2012). OmpA is the principal nonspecific slow porin of Acinetobacter baumannii. J. Bacteriol. 194: 4089-4096.
Sugawara, E., E.M. Nestorovich, S.M. Bezrukov, and H. Nikaido. (2006). Pseudomonas aeruginosa porin OprF exists in two different conformations. J. Biol. Chem. 281: 16220-16229.
Sugawara, E., K. Nagano, and H. Nikaido. (2010). Factors affecting the folding of Pseudomonas aeruginosa OprF porin into the one-domain open conformer. MBio 1:.
Sugawara, E., M. Steiert, S. Rouhani, and H. Nikaido. (1996). Secondary structure of the outer membrane proteins OmpA of Escherichia coli and OprF of Pseudomonas aeruginosa. J. Bacteriol. 178: 6067-6069.
Tachikawa, T. and J. Kato. (2011). Suppression of the temperature-sensitive mutation of the bamD gene required for the assembly of outer membrane proteins by multicopy of the yiaD gene in Escherichia coli. Biosci. Biotechnol. Biochem. 75: 162-164.
Teriete, P., Y. Yao, A. Kolodzik, J. Yu, H. Song, M. Niederweis, and F.M. Marassi. (2010). Mycobacterium tuberculosis Rv0899 Adopts a Mixed alpha/β-Structure and Does Not Form a Transmembrane β-Barrel. Biochemistry 49: 2768-2777.
Vashist, J. and M.R. Rajeswari. (2006). Structural investigations on novel porin, OmpAb from Acinetobacter baumannii. J Biomol Struct Dyn 24: 243-253.
Verma, S., R. Salwan, S. Katoch, L. Verma, R. Chahota, P. Dhar, and M. Sharma. (2016). The relationship between capsular type and OmpA of Pasteurella multocida is associated with the outcome of disease. Microb. Pathog. 101: 68-75. [Epub: Ahead of Print]
Veyron-Churlet, R., B. Brust, L. Kremer, and A.B. Blanc-Potard. (2011). Expression of OmpATb is dependent on small membrane proteins in Mycobacterium bovis BCG. Tuberculosis (Edinb) 91: 544-548.
Walzer, G., E. Rosenberg, and E.Z. Ron. (2006). The Acinetobacter outer membrane protein A (OmpA) is a secreted emulsifier. Environ Microbiol 8: 1026-1032.
White, P.A., S.P. Nair, M.J. Kim, M. Wilson, and B. Henderson. (1998). Molecular characterization of an outer membrane protein of Actinobacillus actinomycetemcomitans belonging to the OmpA family. Infect. Immun. 66: 369-372.
Yaeger, L.N., M.R.M. Ranieri, J. Chee, S. Karabelas-Pittman, M. Rudolph, A.M. Giovannoni, H. Harvey, and L.L. Burrows. (2024). A genetic screen identifies a role for oprF in Pseudomonas aeruginosa biofilm stimulation by subinhibitory antibiotics. NPJ Biofilms Microbiomes 10: 30.
Yang, Y., D. Auguin, S. Delbecq, E. Dumas, G. Molle, V. Molle, C. Roumestand, and N. Saint. (2011). Structure of the Mycobacterium tuberculosis OmpATb protein: a model of an oligomeric channel in the mycobacterial cell wall. Proteins 79: 645-661.
Zhao, X., Y. Cui, Y. Yan, Z. Du, Y. Tan, H. Yang, Y. Bi, P. Zhang, L. Zhou, D. Zhou, Y. Han, Y. Song, X. Wang, and R. Yang. (2013). Outer membrane proteins ail and OmpF of Yersinia pestis are involved in the adsorption of T7-related bacteriophage Yep-phi. J. Virol. 87: 12260-12269.
Zhou J., Wang K., Xu S., Wu J., Liu P., Du G., Li J. and Chen J. (2015). Identification of membrane proteins associated with phenylpropanoid tolerance and transport in Escherichia coli BL21. J Proteomics. 113:15-28.
Examples:

TC#NameOrganismal TypeExample
1.B.6.1.1

Weakly anion-selective OmpA porin OF 346 aas and one N-terminal TMS.  It can exist in two distinct conductance states (Arora et al. 2000), and may function in the transport of phenylpropanoids (resveratrol, naringenin and rutin) (Zhou et al. 2014). Three membrane-bound folding intermediates of OmpA were discovered in folding studies with dioleoylphosphatidylcholine bilayers. A highly synchronized mechanism of secondary and tertiary structure formation, applicable to this and other β-barrel membrane proteins has been described (Kleinschmidt 2006).

Bacteria

OmpA of E. coli (P0A910)

 
1.B.6.1.10

Outer membrane insertion signal domain protein of 190 aas and one N-terminal TMS.  An ortholog in Veillonella parvula is 84% identical, and was considered to be a porin by Poppleton et al. 2017.

Bacteria

OMISD protein of Veillonella atypica

 
1.B.6.1.11

OmpA of 210 aas. The 3-d structure has been solved by NMR (Renault et al. 2010), and its dynamics have been examined (Renault et al. 2009).

Gram-negative bacteria

OmpA of Klebsiella pneumoniae

 
1.B.6.1.12

Omp34 outer membrane porin of 346 aas.  Also known as the Major antigen Fc binding protein (White et al. 1998).

Proteobacteria

Omp34 of Aggregatibacter actinomycetemcomitans (Actinobacillus actinomycetemcomitans) (Haemophilus actinomycetemcomitans)

 
1.B.6.1.13

Putative porin of 253 aas

Actinobacteria

Putative porin of Nocardioidaceae bacterium Broad-1

 
1.B.6.1.14

Outer membrane protein of 638 aas, OmpF

Bacteroidetes

OmpF of Cecembia lonarensis

 
1.B.6.1.15

OmpA/F

Spirochaetes

OmpA/F of Treponema pallidum

 
1.B.6.1.16

OmpA family porin of 410 aas

Proteobacteria

OmpA porin of Phenylobacterium zucineum

 
1.B.6.1.17

Putative OmpF homologue

Spirochaetes

Putative OmpF homologue of Leptospira interrogans

 
1.B.6.1.18

Outer membrane protein of 210 aas and 1 putative N-terminal TMS.

Proteobacteria

OMP of Thiothrix nivea

 
1.B.6.1.19

Outer membrane protein of 218 aas and 8 putative TMSs

Bacteroidetes

OMP of Mariniradius saccharolyticus

 
1.B.6.1.2

OmpF (OprF) porin of 350 aas and 1 N-terminal TMS.  The N-terminal domain has pore activity (Saint et al. 2000).  The protein can exist in multiple conformations of variable conductivities (Nestorovich et al. 2006).  Factors affecting its one-domain open conformer have been studied by Sugawara et al. (2010). OprF is a complement component C3 receptor (Mishra et al. 2015) and is a target of antibacterial drugs (Maccarini et al. 2017). OprF assumes dual conformations and is involved in solute transport, cell envelope integrity, biofilm formation and pathogenesis (Cassin and Tseng 2019). OprF in Pseudomonas aeruginosa is involved in biofilm stimulation by subinhibitory antibiotics (Yaeger et al. 2024).

Bacteria

OmpF (OprF) of Pseudomonas aeruginosa (P13794)

 
1.B.6.1.20

OmpA homologue of 189 aas

Spirochaetes

OmpA homologue of Leptospira biflexa

 
1.B.6.1.21

OmpA-type porin of 160 aas, YfiB The yfiRNB locus in E. coli CFT073 contains genes for YfiN, a diguanylate cyclase, and its activity regulators, YfiR and YfiB.(Raterman et al. 2013).

YfiB of E. coli

 
1.B.6.1.22

Constitutively expressed OmpA of 365 aas (Gao et al. 2015).

OmpA of Shewanella oneidensis

 
1.B.6.1.23

OmpA of 354 aas with 1 N-terminal α-TMS, 10 putative β-TM Strands and a periplasmic C-terminal domain, probably a peptidoglycan-binding domain (Khalid et al. 2008).  Plays a role in virulence (pneumonia in pigs and ruminants) (Verma et al. 2016; Confer and Ayalew 2013) and has been used for vaccine development (Dabo et al. 2008).

OmpA of Pasteurella multocida

 
1.B.6.1.24

Omp38; OmpA of 356 aas and 1 N-terminal TMSs. It is a selective antibiotic transporting porin (Iyer et al. 2018; Jyothisri et al. 1999) and induces apoptosis in human cell lines through caspase-dependent and AIF-dependent pathways. Purified Omp38 enters host cells and localizes to the mitochondria, which presumably leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor) (Choi et al. 2005). It is a virulence factor (Scribano et al. 2024).

omp38 of Acinetobacter baumannii

 
1.B.6.1.25

Putative OmpA porin of 345 aas and one N-terminal TMS. Its gene is adjacent to an autoinducer exporter-like protein (2.A.86.1.11) (Poppleton et al. 2017).

OmpA-like protein of Veillonella parvula

 
1.B.6.1.26

OmpA -like protein of 159 aas and 1 N-terminal TMS, PsaB or YfiB.  It is involved in stress tolerance and negatively correlates to stress tolerance (Scribano et al. 2024).

PsaB of Acinetobacter baumannii

 
1.B.6.1.27

PalA of 157 aas

PalA pf Helicobacter pylori

 
1.B.6.1.3

OmpATb (ArfA). The central domain (residues 73-220) has been reported to exhibit channel activity (Molle et al., 2006). Its expression is dependent on small single TMS membrane proteins which are encoded in a single operon with it (Veyron-Churlet et al., 2011). The rv0899 gene, encoding OmpATb, is part of an operon (rv0899-rv0901) that is required for fast ammonia secretion, pH neutralization, and growth of M. tuberculosis in acidic environments (Song et al. 2011). Homologues are widespread in bacteria with functions in nitrogen metabolism, adaptation to nutrient poor environments, and/or establishing symbiosis with host organisms (Marassi, 2011). The high resolution 3-d structure is known, revealing two independent domains separated by a proline-rich hinge region.The C-terminal domain (OmpATb(198-326)) revealed a module structurally related to other OmpA-like proteins from Gram-negative bacteria, but the N-terminal domain(73-204), which  forms channels in planar lipid bilayers, exhibits a fold, which belongs to the α+β sandwich class fold. It exists in a major monomeric form and a minor oligomeric form yielding rings able to insert into phospholipid membranes (Yang et al. 2011). The OmpA-like domain (residues 196-326) binds M. tuberculosis peptidoglycan. Overexpression in M. bovis or M. smegmatis gives channels with average conductance value of 1,600 +/- 100 pS (Raynaud et al. 2002).

Bacteria

OmpATb of Mycobacterium tuberculosis (P65593)

 
1.B.6.1.4

HMP-AB outer membrane porin, OmpAb or Omp38 (Gribun et al., 2004).  It is the principle porin with an inner diameter of 2 nm which allows transport of cephalothin, cephaloridine, other antibiotics as well as other small molecules across the outer membrane (Sugawara and Nikaido 2012). Structural studies have been reported (Vashist and Rajeswari 2006). It is a secreted emulifier in some strains of Acinetobacter (Walzer et al. 2006). The sequence provided may be slightly incorrect (see the Q6BYW5 sequence of 356 aas).

Bacteria

HMP-AB of Acinetobacter baumannii (Q8KWW6)

 
1.B.6.1.5

The OmpA-OmpF porin (OOP) family member, GmpA (involved in acetic acid fermentation; under quorum sensing control) (Iida et al., 2008). (most similar to 1.B.6.1.4)

Bacteria

GmpA of Gluconacetobacter intermedius (B3A000)

 
1.B.6.1.6Outer membrane protein 40 (Omp40) (PG33)BacteriaPG_0694 of Porphyromonas gingivalis
 
1.B.6.1.7

OmpA homologue

Firmicute with outer membrane

OmpA homologue of Megasphaera elsdenii

 
1.B.6.1.8

OmpA homologue

Firmicute with outer membrane

OmpA homologue of Megasphaera sp. UPII 135-E

 
1.B.6.1.9

OMP_b-br1 family protein

Firmicute with outer membrane

Outer membrane protein of Megasphaera elsdenii

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.10.1

Putative OmpW homologue of 219 aas (Giacani et al. 2015).

Spirochaetes

Putative OmpW homologue of Treponema pallidum

 
1.B.6.10.2

Putative OmpW homologue of 291 aas (Giacani et al. 2015).

Spirochaetes

Putative OmpW homologue of Treponema pallidum

 
1.B.6.10.3

Putative OmpW porin of 211 aas and 8 β-strands

Spirochaetes

Putative OmpW homologue of Treponema azotonutricium

 
1.B.6.10.4

Putative OmpW homologue of 206 aas and 8 β-strands.

Spirochaetes

Putative OmpW homologue of Spirochaeta africana

 
1.B.6.10.5

Putative OmpW homologue of 211 aas

Spirochaetes

OmpW homologue of Borrelia hermsii

 
1.B.6.10.6

Uncharacterized protein of 196 aas.

Spirochaetes

UP of Sphaerochaeta pleomorpha

 
1.B.6.10.7

Uncharacterized protein of 205 aas.

Spirochaetes

UP of Treponema denticola

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.11.1

Putative porin of 357 aas and 1 N-terminal TMS

Porin of Candidatus Methanoperedenaceae archaeon

 
1.B.6.11.2

Uncharacterized protein of 407 aas

UP of Stentor coeruleus

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.12.1

A major outer membrane protein of 298 aas and 1 N-terminal TMS, from Methylacidiphilum fumariolicum SolV (Liu et al. 2023). This porin has a β-barrel structure consisting of ten antiparallel β-sheets and with a small amphipathic N-terminal α-helix in the periplasm. Because M. fumariolicum SolV, lives in a geothermal environment with low pH and high temperatures, this protein may act as barrier to resist the extreme conditions found in its natural environment (Liu et al. 2023).

Major OM Porin, WP_009059494, of Methylacidiphilum fumariolicum SolV

 
1.B.6.12.2

Uncharacterized opacity protein or related surface antigen of 278 aas and 1 N-terminal TMS.  This protein is also distantly related to members of TC family 1.B.49.

UP of a Bradyrhizobium sp. S23321 [Gemmataceae bacterium]

 
1.B.6.12.3

Outer membrane beta-barrel protein of 306 aas and 1 N-terminal TMS. This protein resembles members of TC family 1.B.49. a member of theOMPP1 Superfamily.

OMP of Candidatus Methylacidithermus pantelleriae

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.13.1

Putative lipoprotein, YiaD, of 219 aas with 3 N-terminal TMSs and a C-terminla OmpA peptidoglycan binding domain. When expressed in a multicopy plasmid, its expression supressed the phenotype of a bamD ts mutant (Tachikawa and Kato 2011).

YiaD of E. coli

 
1.B.6.13.2

Uncharacterized protein of 212 aas and at least one N-terminal TMS, possibly plus 2 additional near N-terminal TMSs as well as a C-terminal OmpA peptidoglycan binding domain.

UP of Fusobacterium periodonticum

 
1.B.6.13.3

Uncharacterized protein of 226 aas with 3 N-terminal TMSs and a C-terminal OmpA domain.

UP of Prevotella ruminicola

 
1.B.6.13.4

Putative uncharacterized porin of 368 aas

UP of Bdellovibrio bacteriovorus

 
1.B.6.13.5

ArfA, a member of the OmpA family.  It is of 471 aas with 3 N-terminal TMSs.  It affects cell stiffness, cell shape and virulence (Scribano et al. 2024).

ArfA of Acinetobacter baumannii

 
1.B.6.13.6

OmpA family protein of 191 aas with 1 N-terminal TMS (Hölzer et al. 2025). This protein shows sequence similarity with Pal (TC#2.C.1.2.5; e-25) followed by 1.B.6.13.2 (e-16) and 9.B.153.3.3 (e-15).

OmpA family homolog of Chlamydiifrater phoenicopteri.

 

 
Examples:

TC#NameOrganismal TypeExample
Examples:

TC#NameOrganismal TypeExample
1.B.6.2.1

Outer membrane porin precursor, OmpX (8 TM β-strands). The NMR structures in lipid bilayers has been solved (Mahalakshmi et al., 2007; Mahalakshmi and Marassi, 2008; Fernández et al. 2004). Expression of the encoding gene is induced by acid or base compared to pH 7 (Stancik et al. 2002).

Bacteria

OmpX of E. coli (P0A917)

 
1.B.6.2.10

Outer membrane porin, OmpX of 171 aas (Dupont et al. 2004).

Proteobacteria

OmpX of Enterobacter (Aerobacter) aerogenes

 
1.B.6.2.11

Outer membrane porin, opacity type, of 189 aas

Chlorobi

OMP of Prosthecochloris vibrioformis

 
1.B.6.2.12

Outer membrane porin, opacity type, of 230 aas

Chlorobi

OMP of Chlorobaculum parvum

 
1.B.6.2.13

Putative invasin of 242 aas

Proteobacteria

Putative invasin of E. coli

 
1.B.6.2.14

Uncharacterized protein of 290 aas

Proteobacteria

UP of Nitrobacter hamburgensis

 
1.B.6.2.15

Putative porin of 199 aas

Proteobacteria

Putative porin of Rhodanobacter thiooxydans

 
1.B.6.2.16

Uncharacterized protein of 196 aas

Protetobacteria

UP of Vibrio fischeri

 
1.B.6.2.17

Putative porin of 195 aas

Proteobacteria

Putative porin of Vibrio alginolyticus

 
1.B.6.2.18

Uncharacterized protein of 186 aas

Proteobacteria

UP of Agarivorans albus

 
1.B.6.2.19

Putative porin of 182 aas

Proteobacteria

PP of Grimontia hollisae

 
1.B.6.2.2

The attachment inversion locus (Ail) (Bartra et al., 2007).  Membrane-bound proteins, Ail and OmpF, are involved in the adsorption of T7-related bacteriophage (Zhao et al. 2013).

Proteobacteria

Ail of Yersinia pestis (Q0WCZ9)

 
1.B.6.2.20

Ail/Lom protein of 199 aas

Ail/Lom protein of E. coli

 
1.B.6.2.3Opacity family porin protein

Gram-negative bacterium

UMN179_00549 of Gallibacterium anatis
 
1.B.6.2.4Opacity family porin protein

Gram-negative bacterium

UMN179_00948 of Gallibacterium anatis
 
1.B.6.2.5

Neisserial surface protein A, NspA of 174 aas and 8 TMSs (Hou et al. 2003).

Proteobacteria

NspA of Neisseria meningitidis

 
1.B.6.2.6Porin opacity typeNoneAM202_02155 of Actinobacillus minor 202
 
1.B.6.2.7

Outer membrane porin homolog, but annotated as arginine transporter permease subunit, ArtM, in Uniprot.

None

GGC_0882 of Haemophilus haemolyticus M21621

 
1.B.6.2.8Opa-like protein ANoneE9U_09445 of Moraxella catarrhalis BC8
 
1.B.6.2.9Surface protein ANone

NspA of Neisseria wadsworthii 9715

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.3.1

Putative porin of 197 aas

Verrucomicrobia

PP of Opitutaceae bacterium TAV1

 
1.B.6.3.2

Putative porin of 277 aas

Verrucomicrobia

PP of Coraliomargarita sp. CAG:312

 
1.B.6.3.3

Putative porin

Verruclmicrobia

PP of Opitutus terrae

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.4.1

Putative porin of 183 aas

Proteobacteria

Putative porin of Vibrio parahaemolyticus

 
1.B.6.4.2

Porin of 190 aas and 1 N-terminal TMS.

Porin of Shewanella psychrophila

 
1.B.6.4.3

Porin of 198 aas and 1 N-terminal TMS.

Porin of Pseudoalteromonas luteoviolacea

 
1.B.6.4.4

Porin of 180 aas and 1 N-terminal TMS

Porin of Vibrio caribbeanicus

 
1.B.6.4.5

Porin of 186 aas and 1 N-terminal TMS

Porin of Litorilituus sp. RZ04

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.5.1

Outer membrane protein of 205 aas and 8 putative TMSs.

Fibrobacteres

OMP of Fibrobacter succinogens

 
1.B.6.5.2

Outer membrane protein of 197 aas and 8 putative TMSs.

Bibrobacteres

OMP of Fibrobacter succinogenes

 
1.B.6.5.3

Outer membrane protein of 534 aas and 6 - 22 beta strands.

Spirochaetes

OMP of Turneriella parva

 
1.B.6.5.4

Outer membrane protein of 211 aas and 8 beta strands.

Proteobacteria

OMP of Myxococcus xanthus

 
1.B.6.5.5

Outer membrane protein of 201 aas and 9 putative beta strands.

Proteobacteria

OMP of Vibrio tubiashii

 
1.B.6.5.6

Outer membrane protein, OmpA of 196 aas and 8 putative TMSs

Proteobacteria

OmpA of Aliivibrio salmonicida

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.6.1

Outer membrane protein of 201 aas and 8 putative β-TMSs.

Bacteroidetes

OMP of Cyclobacterium marinum

 
1.B.6.6.10

Putative porin of 157 aas and 8 beta strands

Bacteroidetes

Putative porin of Paludibacter propionicigenes

 
1.B.6.6.11

Uncharacterized protein of 208 aas.

Bacteroidetes

UP of Pedobacter saltans

 
1.B.6.6.12

Putative porin of 192 aas

Bacteroidetes

Putative porin of Capnocytophaga sputigena

 
1.B.6.6.2

Outer membrane protein of 224 aas and 8 TMSs

Bacteroidetes

OMP of Dyadobacter fermentans

 
1.B.6.6.3

Outer membrane protein of 204 aas and 8 TMSs

Bacteroidetes

OMP of Solitalea canadensis

 
1.B.6.6.4

Outer membrane protein of 221 aas and 8 TMSs

Bacteroidetes

OMP of Psychroflexus torquis

 
1.B.6.6.5

Outer membrane protein of 222 aas

Bacteroidetes

OMP of Echinicola vietnamensis

 
1.B.6.6.6

Outer membrane protein of 199 aas

Bacteroidetes

OMP of Chitinophaga pinensis

 
1.B.6.6.7

Porin of 193 aas and 8 beta strands

Bacteroidetes

Porin of Flavobacterium johnsoniae

 
1.B.6.6.8

Porin of 180 aas and 8 beta strands

Nitrospirae

Porin of Candidatus Nitrospira defluvii

 
1.B.6.6.9

Porin of 207 aas and 8 beta strands

Proteobacteria

Porin of Myxococcus xanthus

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.7.1

Outer membrane protein of 257 aas and 8 beta strands

Bacteroidetes

OMP of Bacteroides fragilis

 
1.B.6.7.2

Porin of 275 aas and 1 N-terminal TMS

Porin of Bacteroides xylanisolvens

 
1.B.6.7.3

DUF4421 domain-containing protein of 334 aas and 1 N-terminal TM

Putative porin of Flavobacterium rivuli

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.8.1

Porin of 224 aas and 8 beta strands, TtoA (Estrada Mallarino et al. 2015).  The crystal structure is known (3DZM) (Nesper et al. 2008). The 2.8 Å structure reveals a transmembrane 8 stranded β-barrel, an extracellular cation-binding region and an external 5-β stranded sheet (Brosig et al. 2009).

Thermus/Deinococcus

Porin of Thermus thermophilus

 
1.B.6.8.2

Putative porin of 222 aas.

Thermus/Deinococcus

Putative porin of Deinococcus geothermalis

 
1.B.6.8.3

Putative porin of 227 aas and 1 N-terminal TMS

Porin of Ignavibacterium album

 
Examples:

TC#NameOrganismal TypeExample
1.B.6.9.1

Uncharacterized protein of 186 aas.

Ignavibacteriae

UP of Ignavibacterium album

 
1.B.6.9.2

Uncharacterized putative porin protein of 189 aas.

Bacteroidetes

UP of Owenweeksia hongkongensis

 
1.B.6.9.3

Uncharacterized putative porin of 205 aas

Bacteroidetes

Putative porin of Owenweeksia hongkongensis

 
1.B.6.9.4

Uncharacterized protein of 167 aas

Bacteroidetes

UP of Elizabethkingia anophelis