1.B.1 The General Bacterial Porin (GBP) Family

OMP porins are present in the outer membranes of Gram-negative bacteria, mitochondria and plastids. They catalyze the energy-independent facilitation of small (Mr of <1000 Da) molecules across the outer membranes of bacteria and organelles with variable degrees of selectivity. The structurally characterized members of this functional superfamily usually consist of homotrimeric proteins with subunits that are of 250-450 amino acyl residues in length. The high resolution three-dimensional structures of several of these proteins are known. These proteins include OmpC, OmpF and PhoP of E. coli. They form 16-stranded antiparallel β-barrel structures with all β-strands hydrogen-bonded to their nearest neighbors along the chain. Each trimer consists of three channels, each with the β-barrel perpendicular to the plane of the membrane. Polypeptide loops lining the inner barrel wall restrict the channel width, thereby defining the diffusion properties of the pore. Some porins are cation-selective, others are anion-selective and still others are selective for specific compounds (e.g., sugars, nucleotides, phosphate, pyrophosphate). Sequence comparisons and three-dimensional structural analyses suggest that many of the families described under category 1.B are related (see porin superfamilies in TCDB and (Reddy and Saier 2016).

β-barrel membrane proteins perform a variety of functions, such as mediating non-specific, passive transport of ions and small molecules, selectively passing molecules like maltose and sucrose, and can form voltage dependent anion channels. Understanding the structural features of β-barrel membrane proteins and detecting them in genomic sequences are challenging tasks in structural and functional genomics. With the survey of experimentally known amino acid sequences and structures, the characteristic features of amino acid residues in β-barrel membrane proteins and novel parameters for understanding their folding and stability have been described by Gromiha and Suwa (2007). Statistical methods and machine learning techniques discriminate β-barrel membrane proteins from other folding types of globular and membrane proteins. Different methods including hydrophobicity profiles, rule based approach, amino acid properties, neural networks, hidden Markov models etc., predict membrane spanning segments of β-barrel membrane proteins. Discrimination techniques for detecting β-barrel membrane proteins in genomic sequences are discussed by Gromiha and Suwa (2007).

Vibrio furnissii possesses an outer membrane porin that is induced by β1,4-N-acetyl glucosamine (GlcNAc) oligomers of two to six sugar units, hydrolysis products of chitinase action on chitin (Keyhani et al., 2000). This porin is required for growth on (GlcNAc)3, and it transports acetylated chitobiose analogues, suggesting that it is specific for these oligosaccharides. It forms a subfamily (TC #1.B.1.7.1) of the GBP family. Another porin, OmpP2 of Haemophilus influenzae (TC # 1.B.1.3.2), shows specificity for nicotinamide-derived nucleotide substrates (Andersen et al., 2003).

Gram-negative Legionella pneumophila produces a siderophore (legiobactin) that promotes lung infection. lbtA and lbtB are required for the synthesis and secretion of legiobactin. An iron-repressed gene (lbtU) is directly upstream of the lbtAB-containing operon. LbtU is an outer membrane protein consisting of a 16-stranded transmembrane β-barrel, multiple extracellular domains, and short periplasmic tails. Although replicating normally, lbtU mutants, like lbtA mutants, were impaired for growth on iron-depleted media and would not take up Fe3+ legiobactin. It is the Legionella siderophore receptor.

The generalized transport reaction catalyzed by porins is:

Solute (out) Solute (in)



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

 

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Ye, Y., L. Xu, Y. Han, Z. Chen, C. Liu, and L. Ming. (2018). Mechanism for carbapenem resistance of clinical Enterobacteriaceae isolates. Exp Ther Med 15: 1143-1149.

Zachariae, U., T. Klühspies, S. De, H. Engelhardt, and K. Zeth. (2006). High resolution crystal structures and molecular dynamics studies reveal substrate binding in the porin Omp32. J. Biol. Chem. 281: 7413-7420.

Examples:

TC#NameOrganismal TypeExample
1.B.1.1.1

OmpF general porin. OmpF can deliver peptides of >6 KDa (epitopes) including protamine, through the pore lumen from the periplasm to the outside (Housden et al., 2010; Ghale et al. 2014).  For cephalosporin antibiotics, the interaction strength series is ceftriaxone > cefpirome > ceftazidime (Lovelle et al. 2011).  An unfolded protein such as colicin E9 can thread through OmpF from the outside to reach the periplasm (Housden et al. 2013).  Polynucleotides can pass through OmpF (Hadi-Alijanvand and Rouhani 2015). LPS influences the movement of bulk ions (K+ and Cl-), but the ion selectivity of OmpF is mainly affected by bulk ion concentrations (Patel et al. 2016).  OMPs such as OmpF cluster into islands that restrict their lateral mobility, while IMPs generally diffuse throughout the cell. Rassam et al. 2018 demonstrated that when transient, energy-dependent transmembrane connections are formed, IMPs become subjugated by the inherent organisation of OMPs, and that such connections impact IMP function. They showed that while establishing a translocon for import, colicin ColE9 sequesters the IMPs of the proton motive force (PMF)-linked Tol-Pal complex into islands mirroring those of colicin-bound OMPs. Through this imposed organisation, the bacteriocin subverts the outer-membrane stabilizing role of Tol-Pal, blocking its recruitment to cell division sites and slowing membrane constriction. The ordering of IMPs by OMPs via an energised inter-membrane bridge represents an emerging functional paradigm in cell envelope biology (Rassam et al. 2018). Colicin E9 (ColE9) disordered regions exploit OmpF for direction-specific binding, which ensures the constrained presentation of an activating signal within the bacterial periplasm (Housden et al. 2018). Anionic lipid binding can prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways (Liko et al. 2018). OmpF may be the major route of D-lactate/D-3-hydroxybutyrate oligo-ester secretion (Utsunomia et al. 2017).

Proteobacteria

OmpF of E. coli (P02931)

 
1.B.1.1.10

Putative porin

γ-Proteobacteria

Putative porin of Dickeya dadantii

 
1.B.1.1.11

Porin OmpPst1.  Transports carbapenem antibiotics imipenem will slow flux and meropenem with rapid flux in a reconsituted ion conductance system (Bajaj et al. 2012).

Proteobacteria

OmpPst1 of Providencia stuartii

 
1.B.1.1.12

High conductance Omp35 (OmpK35; OmpF) porin.  Expression levels are important for beta-lactam/cephalosporin resistance (Bornet et al. 2004).  95% identical to the Klebsiella pneumoniae orthologue, OmpK35 (Taherpour and Hashemi 2013). In K. pneumoniae, colistin-based combination therapy with a carbapenem and/or tigecycline was associated with significantly decreased mortality rates due in part to synergistic induction of porins K35 and K36 (Stein et al. 2015). They influence imipenem susceptibility as well (Wassef et al. 2015). These two porins play roles in conferring carbapenem resistance in K. pneumoniae (Hamzaoui et al. 2018; Ye et al. 2018).

Proteobacteria

Omp35 of Enterobacter (Aerobacter) aerogenes

 
1.B.1.1.13

Omp36 (OmpC) porin of 375 aas (et al. 2001; Bornet et al. 2004). Mutations affect beta-lactam and carbapenem (imipenem) sensitivity (Pavez et al. 2016).

Proteobacteria

Omp36 of Enterobacter (Aerobacter) aerogenes

 
1.B.1.1.14

Major voltage-independent outer membrane porin, OmpH (Chevalier et al. 1993).  A 3D model was obtained using in silico modeling.  OmpH is probably a homotrimeric, 16 stranded, β-barrel porin involved in the non-specific transport of small, hydrophilic molecules, serving osmoregulatory functions (Ganguly et al. 2015).

Proteobacteria

OmpH of Pasteurella multocida

 
1.B.1.1.15

OmpU porin (cation-selective; PK/PCl = 14; bile salt inducible) (low permeability to bile) (Simonet et al., 2003). OmpU influences sensitivities to β-lactam antibiotics and sodium deoxycholate induction of biofilm formation and growth on large sugars (Pagel et al., 2007).   The effective pore radus is 0.55 nm which increases with acidic pH but decreases with increasing ionic strength (Duret and Delcour 2010). OmpU induces target animal cell death after it inserts into host mitochondrial membranes (Gupta et al. 2015). The high resolution structures of OmpT and OmpU, the two major porins in V. cholerae, have been determined, and both have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels (Pathania et al. 2018).

Bacteria

OmpU of Vibrio cholerae

 
1.B.1.1.16

OmpC of 367 aas (Vostrikova et al. 2013).

Proteobacteria

OmpC of Yersinia enterocolitica

 
1.B.1.1.17

OmpF of 243 aas (Vostrikova et al. 2013).

Proteobacteria

OmpF of Yersinia enterocolitica

 
1.B.1.1.18

Putative porin of 381 aas

Proteobacteria

PP of Klebsiella pneumoniae

 
1.B.1.1.19

Outer membrane porin, KpnO, OmpCKP or OmpK36 of 367 aas.  Loss causes increased drug (e.g., carbapenem and imipenem, but not colistin) resistance (Wassef et al. 2015Jasim et al. 2018) decreased virulence and increased susceptibility to gastrointestinal stress (García-Sureda et al. 2011; Srinivasan et al. 2012).  Expression is under PhoBR control.  Porin deficiency is a widespread phenomenon, probably accounting for elevated ertapenem resistance (Wise et al. 2018).

Proteobacteria

KpnO of Klebsiella pneumoniae

 
1.B.1.1.2

PhoE phosphoporin. The 3-d structure is available (PDB#1PHO)

Bacteria

PhoE of E. coli

 
1.B.1.1.20

Outer membrane porin 1, OmpPst1 or Omp-Pst1.  Transports beta lactams with decreased efficiency in the order of ertapenem > cefepime > cefoxitin (Tran et al. 2010).  93% identical in sequence to 1.B.1.1.11. Voltage-gating of this porin and porin 2 (TC# 1.B.1.1.24) from the same organism have been analyzed (Song et al. 2015). Facing channels are open in any two adjacent porin structures, suggesting that dimers and trimers not only promote cell-to-cell contact but also contribute to intercellular communication (El-Khatib et al. 2018).

Proteobacteria

OmpPst1 of Providencia stuartii

 
1.B.1.1.21

Outer membrane non-specific porin, OmpN or OmpS2, under the control of SoxS, and coregulated with the ydbK gene encoding pyruvate:flavodoxin oxidoreductase which plays a role in protection against oxidative stress (Prilipov et al. 1998; Fàbrega et al. 2012). MicC sRNA acts together with the σE envelope stress response pathway to control OmpN levels in response to β-lactam antibiotics (Dam et al. 2017).

Proteobacteria

OmpN of E. coli

 
1.B.1.1.22

Outer membrane porin of 383 aas, OmpS2.  Activated by OmpR and LeuO (Fernández-Mora et al. 2004).

Proteobacteria

OmpS2 of Salmonella typhi

 
1.B.1.1.23

Outer membrane trimeric porin, OmpY (also called OmpN or OmpC2) of 360 aas. The effects of the length of loop L2 on function and stability have been studied (Solov'eva et al. 2017).

Proteobacteria

OmpY of Yersinia pseudotuberculosis

 
1.B.1.1.24

Porin 2 (Omp-Pst2 or OmpPst2) of 365 aas.  Voltage gating is observed for Omp-Pst2, where the binding of cations in-between L3 and the barrel wall results in exposing a conserved aromatic residue in the channel lumen, thereby halting ion permeation. Comparison of Omp-Pst1 (TC# 1.B.1.1.20) with Omp-Pst2 suggested that their differing sensitivities to voltage is encoded in the hydrogen-bonding network anchoring L3 onto the barrel wall. The strength of this network governs the probability of cations binding behind L3. That Omp-Pst2 gating is observed only when ions flow against the electrostatic potential gradient of the channel suggests a possible role for this porin in the regulation of charge distribution across the outer membrane and bacterial homeostasis (Song et al. 2015).

Proteobacteria

OmpPst2 of Providenica stuartii

 
1.B.1.1.25

Anion-selective, voltage-sensitive porin, VCA_1008, of 331 aas with a pore exclusion limit of 6.9 nm (Goulart et al. 2015).

VCA_1008 of Vibrio cholerae

 
1.B.1.1.26

The mature outer membrane protein, OmpC of 342 aas.  Elicits an immune response (Yadav et al. 2016).

OmpC of Aeromonas hydrophila

 
1.B.1.1.27

Outer membrane porin, OmpS1 of 394 aas.  mutants defective for OmpS1 are attenuated for virulence in mice (Rodríguez-Morales et al. 2006).

OmpS1 in Salmonella enterica serovar Typhi

 
1.B.1.1.3

OmpC general porin.  Expression of OmpC and OmpF is reciprocally regulated by the EnvZ/OmpR sensor kinase/response regulator system (Egger et al. 1997).  Mutants isolated from patients with MDR E. coli, resistant to several antibiotics, showed decreased permeability to these antibiotics (Lou et al. 2011). The diffusion route of the fluoroquinolone, enrofloxacin, through the OmpC porin has been reported (Prajapati et al. 2018).

Bacteria

OmpC of E. coli

 
1.B.1.1.4

Weakly anion-selective NmpC (OmpD) porin (Prilipov et al. 1998).  Transports methyl benzyl viologen, ceftriaxone and hydrogen peroxide in Salmonella species (Hu et al. 2011; Calderón et al. 2010).

Bacteria

NmpC of E. coli

 
1.B.1.1.5

LC (lysogenic conversion) porin.  Can replace OmpC and OmpF and is therefore probably non-selective (Fralick et al. 1990).  Synthesis is subject to catabolite repression mediated by the cyclicAMP receptor protein, CRP (Blasband and Schnaitman 1987).

 

Phage

LC porin of phage PA-2

 
1.B.1.1.6

Major outer membrane porin, OpnP.  Probably orthologous to the E. coli OmpF.  Expression of the opnP gene is activated by EnvZ and regulated by temperatur (Forst et al. 1995; Forst and Tabatabai 1997).

Bacteria

OpnP of Xenorhabdus nematophilus

 
1.B.1.1.7

ComP porin.  A virulence factor essential for cytotoxicity and apoptosis by this enteric pathogen (Tsugawa et al., 2008)

Bacteria

ComP of Plesiomonas shigelloides (A0JCJ5)

 
1.B.1.1.8Trimeric 16 TMS non-specific porin, Omp-EA (Elazer et al., 2007)BacteriaOmp-EA of Erwinia amylovora (A0RZH5)
 
1.B.1.1.9

OmpU porin (weakly cation-selective; expression is induced by bile salts; OmpU mediates bile salt resistance) (Wang et al., 2003).

Bacteria

OmpU of Listonella (Vibrio) anguillarum (Q8GD13)

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.10.1

Legiobactin receptor, LbtU of 361 aas with one N-terminal TMS and 16 predicted beta-strands (Chatfield et al., 2011).

Bacteria

LbtU of Legionella pneumoniae (E2JEY3)

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.11.1

Putative porin (based on homology) of 375 aas

Proteobacteria

Putative porin of Helicobacter hepaticus

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.12.1

Porin of 194 aas and 10 transmembrane β-strands, Omp1X (Park et al. 2014).

Proteobacteria

Porin of Xanthomonas oryzae

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.2.1

Omp25 of 255 aas.  Associates with CarO (Siroy et al. 2005).

Proteobacteria

Omp25 of Acidetobacter baumannii

 
1.B.1.2.2

Putative porin of 251 aas

Proteobacteria

PP of Shewanella piezotolerans

 
1.B.1.2.3

Putative porin of 306 aas

Proteobacteria

PP of Colwellia psychrerythraea (Vibrio psychroerythus)

 
1.B.1.2.4

Outer membrane porin, Omp33 or Omp33-36.  This protein is a virulence factor and induces apoptosis in the host (Rumbo et al. 2014; Smani et al. 2013). It is involved in carbapenem resistance and is highly polymorphic (Novović et al. 2018).

Proteobacteria

Omp33-36 of Acinetobacter baumannii

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.3.1Omp2 porinBacteriaOmp2 of Haemophilus influenzae
 
1.B.1.3.2

OmpP2 porin (transports NAD and NMN; transport Km=5 mM; may also serve as a general diffusion porin) (Andersen et al., 2003).  Its solute transport activity with size exclusion limit has been described (Kattner et al. 2015).

Bacteria

OmpP2 of Haemophilus influenzae (Q48217)

 
1.B.1.3.3

Putative porin

γ-Proteobacteria

Putative porin of Haemophilus parainfluenzae

 
1.B.1.3.4

Putative porin

β-Proteobacteria

Putaive porin of Neisseria sp.

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.4.1Omp porinBacteriaOmp porin of Bordetella pertussis
 
1.B.1.4.2Phthalate porin, OphP (Chang et al. 2009).

 Bacteria

OphP of Burkholderia capacia (C0LZS0)

 
1.B.1.4.3

Porin of 38 KDa,Omp38 in Burkholderia pseudomallei, the causative agent of melioidosis, an infectious disease of animals and humans. MDR can be due to mutations in Omp38.  Ion current blockages of reconstituted Omp38 by seven antimicrobial agents occurred in a concentration-dependent manner with the translocation on-rate following the order: norfloxacin>ertapenem>ceftazidime>cefepime>imipenem>meropenem>penicillin G (Suginta et al. 2011).  Also allows transport of neutral sugars and numerous antimicrobial agents including cephalosporin and carbapenem (Aunkham et al. 2014).

Proteobacteria

Omp38 of Burkholderia pseudomallei

 
1.B.1.4.4

Outer membrane porin of 353 aas (Brunen et al. 1991).

Proteobacteria

OMP of Acidovorax delafieldii

 
1.B.1.4.5

Porin-like protein

Chlorobi

Porin of Chlorobium phaeobacteroides

 
1.B.1.4.6

Putative porin of 248 aas

Proteobacteria

PP of Burkholderia cepacia (T0ET67)

 
1.B.1.4.7

Outer membrane porin, OMPNK8 of 380 aas. Probably involved in transport of and chemotaxis toward β-ketoadipate; encoded by a gene (orf1) on a megaplasmid (pNK8) that carries the gene cluster (orf1-tfdT-CDEF), encoding chlorocatechol-degrading enzymes. orf1 is induced by the presence of 3-chlorobenzoate as is the tfd operon (Yamamoto-Tamura et al. 2015).

OMPNK8 of Burkholderia sp. NK8

 
1.B.1.4.8

Outer membrane porin of 394 aas and 16 predicted beta strands, isolated from an endosymbiont of a  trypanosomatid protozoan (Andrade et al. 2011).

Porin of an endosymbiont of Crithidia deanei

 
1.B.1.4.9

OmpQ porin of 364 aas

OmpQ of Bordetella parapertussis

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.5.1

Oma1 porin (Class 1) (Tanabe et al., 2010)

Bacteria

Oma1 of Neisseria gonorrhoeae

 
1.B.1.5.2

PorA porin, cation selective at pH > 6; anion selective at pH < 4 (a continuum electrodiffusion model accounts for the results) (Cervera et al., 2008)

Bacteria

PorA of Neisseria meningitidis

 
1.B.1.5.3Major outer membrane protein IB (OMB) (slightly cation-selective porin) BacteriaOMB of Neisseria sicca
 
1.B.1.5.4

PorB porin (Song et al. 1998; Tanabe et al., 2010). The 2.3 Å structure has been determined by x-ray crystallography. There are three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one tranports cations nonselectively, and one facilitates the specific uptake of sugars (Kattner et al. 2012). Regulated by ATP binding (Tanabe et al., 2010).  Exhibits voltage-dependent closure (Jadhav et al. 2013). Its unique solute transport activity with size exclusion limit has been described (Kattner et al. 2015).

Bacteria

PorB porin of Neisseria meningitidis

 
1.B.1.5.5

PorB (Class 2). The 2.3 Å structure has been determined by x-ray crystallography. There are three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one tranports cations nonselectively, and one facilitates the specific uptake of sugars. Regulated by ATP binding (Tanabe et al., 2010).  Exhibits voltage-dependent closure (Jadhav et al. 2013).

Bacteria

PorB porin of Neisseria meningitidis (Q51271)

 
1.B.1.5.6

Porin

Acidobacteria

Porin of Holophaga foetida

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.6.1

Anion-selective porin protein 32, Omp32.  The structure is known to 1.5 Å resolution (Zachariae et al. 2006).

Bacteria

Porin protein 32 of Comamonas (Delftia) acidovorans

 
1.B.1.6.2

Outer membrane porin of 304 aas (Brunen et al. 1991).

Proteobacteria

OMP of Acidovorax delafieldii

 
1.B.1.6.3

Outer membrane porin of 319 aas (Brunen et al. 1991).

Proteobacteria

OMP of Acidovorax delafieldii

 
1.B.1.6.4

Outer membrane porin of 313 aas

Chrysiogenetes

Porin of Desulfurispirillum indicum

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.7.1

Chitoporin, ChiP (Keyhani et al., 2000).

Bacteria

ChiP of Vibrio furnissii

 
1.B.1.7.2

Sugar-specific chitoporin of 375 aas, ChiP.  The best substrate is chitohexose, but ChiP  transports a variety of chitooligosaccharides.  Trp136 is important for the binding affinity for chitohexaose (Chumjan et al. 2015). X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides have been solved (Aunkham et al. 2018). Structures without bound sugar reveal a trimeric assembly with an unprecedented closing of the transport pore by the N-terminus of a neighboring subunit. Substrate binding ejects the pore plug to open the transport channel.The structures explain the exceptional affinity of ChiP for chito-oligosaccharides and point to an important role of the N-terminal gate in substrate transport (Aunkham et al. 2018).

Proteobacteria

ChiP of Vibrio harveyi

 
Examples:

TC#NameOrganismal TypeExample
1.B.1.8.1

Low ion selective porin (PK/PCl = 4), OmpT (high permeability to bile) (Simonet et al., 2003). OmpT has an effective radius of 0.43nm, and acidic pH, high ionic strength, or exposure to polyethyleneglycol stabilizes a less conductive state (Duret & Delcour, 2010).  It binds the biofilm matrix protein, Bap1, which influences antimicrobial peptide (polymyxin B and LL-37) resistance (Duperthuy et al. 2013). The high resolution structures of OmpT and OmpU, the two major porins in V. cholerae, have been determined, and both have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels (Pathania et al. 2018).

Bacteria

OmpT of Vibrio cholerae (AAC28105)

 
1.B.1.8.2Putative uncharacterized proteinNoneTresu_2327 of Treponema succinifaciens
 
1.B.1.8.3Porin-like protein H (37 kDa outer membrane protein)NoneompH of Photobacterium profundum )
 
Examples:

TC#NameOrganismal TypeExample
1.B.1.9.1The outer membrane porin, M35 (Easton et al., 2005)BacteriaM35 of Moraxella catarrhalis (AAX99225)
 
1.B.1.9.2

Major porin of 369 aas, involved in anaerobic respiration, positively regulated by both CRP and FNR, OmpS38 or Omp35 (Gao et al. 2015). 

OmpS38 of Shewanella oneidensis