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.
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.
Weakly anion-selective OmpA porin. Can exist in two distinct conductance states (Arora et al. 2000). 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).
OmpA of E. coli (P0A910)
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.
OMISD protein of Veillonella atypica
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).
OmpA of Klebsiella pneumoniae
Omp34 outer membrane porin of 346 aas. Also known as the Major antigen Fc binding protein (White et al. 1998).
Omp34 of Aggregatibacter actinomycetemcomitans (Actinobacillus actinomycetemcomitans) (Haemophilus actinomycetemcomitans)
Putative porin of 253 aas
Putative porin of Nocardioidaceae bacterium Broad-1
Outer membrane protein of 638 aas, OmpF
OmpF of Cecembia lonarensis
OmpA/F of Treponema pallidum
OmpA family porin of 410 aas
OmpA porin of Phenylobacterium zucineum
Putative OmpF homologue
Putative OmpF homologue of Leptospira interrogans
Outer membrane protein of 210 aas and 8 putative TMSs
OMP of Thiothrix nivea
Outer membrane protein of 218 aas and 8 putative TMSs
OMP of Mariniradius saccharolyticus
OmpF (OprF) porin. 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).
OmpF (OprF) of Pseudomonas aeruginosa (P13794)
OmpA homologue of 189 aas
OmpA homologue of Leptospira biflexa
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
Constitutively expressed OmpA of 365 aas (Gao et al. 2015).
OmpA of Shewanella oneidensis
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
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).
omp38 of Acinetobacter baumannii
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
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).
OmpATb of Mycobacterium tuberculosis (P65593)
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).
HMP-AB of Acinetobacter baumannii (Q8KWW6)
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)
GmpA of Gluconacetobacter intermedius (B3A000)
Firmicute with outer membrane
OmpA homologue of Megasphaera elsdenii
Firmicute with outer membrane
OmpA homologue of Megasphaera sp. UPII 135-E
OMP_b-br1 family protein
Firmicute with outer membrane
Outer membrane protein of Megasphaera elsdenii
Putative OmpW homologue of 219 aas (Giacani et al. 2015).
Putative OmpW homologue of Treponema pallidum
Putative OmpW homologue of 291 aas (Giacani et al. 2015).
Putative OmpW homologue of Treponema pallidum
Putative OmpW porin of 211 aas and 8 β-strands
Putative OmpW homologue of Treponema azotonutricium
Putative OmpW homologue of 206 aas and 8 β-strands.
Putative OmpW homologue of Spirochaeta africana
Putative OmpW homologue of 211 aas
OmpW homologue of Borrelia hermsii
Uncharacterized protein of 196 aas.
UP of Sphaerochaeta pleomorpha
Uncharacterized protein of 205 aas.
UP of Treponema denticola
Putative porin of 357 aas and 1 N-terminal TMS
Porin of Candidatus Methanoperedenaceae archaeon
Outer membrane porin precursor, OmpX (8 TM β-strands) (NMR structures in lipid bilayers solved (Mahalakshmi et al., 2007; Mahalakshmi and Marassi, 2008)). Expression of the gene is induced by acid or base compared to pH 7 (Stancik et al. 2002).
OmpX of E. coli (P0A917)
Outer membrane porin, OmpX of 171 aas (Dupont et al. 2004).
OmpX of Enterobacter (Aerobacter) aerogenes
Outer membrane porin, opacity type, of 189 aas
OMP of Prosthecochloris vibrioformis
Outer membrane porin, opacity type, of 230 aas
OMP of Chlorobaculum parvum
Putative invasin of 242 aas
Putative invasin of E. coli
Uncharacterized protein of 290 aas
UP of Nitrobacter hamburgensis
Putative porin of 199 aas
Putative porin of Rhodanobacter thiooxydans
Uncharacterized protein of 196 aas
UP of Vibrio fischeri
Putative porin of 195 aas
Putative porin of Vibrio alginolyticus
Uncharacterized protein of 186 aas
UP of Agarivorans albus
Putative porin of 182 aas
PP of Grimontia hollisae
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).
Ail of Yersinia pestis (Q0WCZ9)
Ail/Lom protein of 199 aas
Ail/Lom protein of E. coli
Neisserial surface protein A, NspA of 174 aas and 8 TMSs (Hou et al. 2003).
NspA of Neisseria meningitidis
NspA of Neisseria wadsworthii 9715
Putative porin of 197 aas
PP of Opitutaceae bacterium TAV1
Putative porin of 277 aas
PP of Coraliomargarita sp. CAG:312
PP of Opitutus terrae
Putative porin of 183 aas
Putative porin of Vibrio parahaemolyticus
Porin of 190 aas and 1 N-terminal TMS.
Porin of Shewanella psychrophila
Porin of 198 aas and 1 N-terminal TMS.
Porin of Pseudoalteromonas luteoviolacea
Porin of 180 aas and 1 N-terminal TMS
Porin of Vibrio caribbeanicus
Porin of 186 aas and 1 N-terminal TMS
Porin of Litorilituus sp. RZ04
Outer membrane protein of 205 aas and 8 putative TMSs.
OMP of Fibrobacter succinogens
Outer membrane protein of 197 aas and 8 putative TMSs.
OMP of Fibrobacter succinogenes
Outer membrane protein of 534 aas and 6 - 22 beta strands.
OMP of Turneriella parva
Outer membrane protein of 211 aas and 8 beta strands.
OMP of Myxococcus xanthus
Outer membrane protein of 201 aas and 9 putative beta strands.
OMP of Vibrio tubiashii
Outer membrane protein, OmpA of 196 aas and 8 putative TMSs
OmpA of Aliivibrio salmonicida
Outer membrane protein of 201 aas and 8 putative β-TMSs.
OMP of Cyclobacterium marinum
Putative porin of 157 aas and 8 beta strands
Putative porin of Paludibacter propionicigenes
Uncharacterized protein of 208 aas.
UP of Pedobacter saltans
Putative porin of 192 aas
Putative porin of Capnocytophaga sputigena
Outer membrane protein of 224 aas and 8 TMSs
OMP of Dyadobacter fermentans
Outer membrane protein of 204 aas and 8 TMSs
OMP of Solitalea canadensis
Outer membrane protein of 221 aas and 8 TMSs
OMP of Psychroflexus torquis
Outer membrane protein of 222 aas
OMP of Echinicola vietnamensis
Outer membrane protein of 199 aas
OMP of Chitinophaga pinensis
Porin of 193 aas and 8 beta strands
Porin of Flavobacterium johnsoniae
Porin of 180 aas and 8 beta strands
Porin of Candidatus Nitrospira defluvii
Porin of 207 aas and 8 beta strands
Porin of Myxococcus xanthus
Outer membrane protein of 257 aas and 8 beta strands
OMP of Bacteroides fragilis
Porin of 275 aas and 1 N-terminal TMS
Porin of Bacteroides xylanisolvens
DUF4421 domain-containing protein of 334 aas and 1 N-terminal TM
Putative porin of Flavobacterium rivuli
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).
Porin of Thermus thermophilus
Putative porin of 222 aas.
Putative porin of Deinococcus geothermalis
Putative porin of 227 aas and 1 N-terminal TMS
Porin of Ignavibacterium album
Uncharacterized protein of 186 aas.
UP of Ignavibacterium album
Uncharacterized putative porin protein of 189 aas.
UP of Owenweeksia hongkongensis
Uncharacterized putative porin of 205 aas
Putative porin of Owenweeksia hongkongensis
Uncharacterized protein of 167 aas
UP of Elizabethkingia anophelis