| 1.B.14 The Outer Membrane Receptor (OMR) Family
The OMR family includes a large number of sequenced Gram-negative bacterial outer membrane proteins which form transmembrane pores and transport relatively large molecules from the external milieu to the periplasm in an energized process. Although represented in cyanobacteria, no OMR member has been identified in a Gram-positive bacterium, an archaeon or a eukaryote. Energization of transport across the outer membrane requires a heterotrimeric complex of proteins, the TonB-ExbB-ExbD complex, or in some cases, the TolA-TolQ-TolR complex (TC #10.6). Energization requires the proton motive force (pmf) across the cytoplasmic membrane. In the absence of a pmf or one of the three energy coupling proteins of the complex, the receptor binds its substrate, but transport does not occur. Substrates transported by OMR family members include iron-siderophore complexes, vitamin B12, Cu2+, colicins (group B colicins are transported via TonB-dependent receptors while group A colicins are transported via TolA-dependent receptors), and the DNA of various phage. OMR proteins are also essential for the utilization of iron from eukaryotic proteins such as transferrin, hemoglobin and hemin. The vitamin B12, and iron-siderophore receptors feed into ABC-type permeases (TC #3.A.1.13 and 3.A.1.14) for transport across the cytoplasmic membrane. Alteration (e.g., small internal deletions) of some OMR members can convert them into diffusion channels. Normally, they probably form ligand-specific and energy-gated pores through the outer membranes of Gram-negative bacteria. However, the fact that minor genetic changes result in the generation of diffusion channels suggests that these proteins form large porin-like β-barrel structures.
The three-dimensional structure of one OMR family member, FhuA (TC #1.B.14.1.4), has been elucidated in two conformations, one with and one without bound ferrichrome-iron, both at about 2.6 Å resolution (see Ferguson and Deisenhofer (2004) for a review summarizing function/structure relationships). FhuA is a β-barrel composed of 22 antiparallel β-strands. In contrast to the trimeric arrangement seen in many porins, FhuA is monomeric. Located within the β-barrel is a domain called the 'cork' which consists of a four-stranded β-sheet and four short α-helices. The cork closes the channel, but without the cork, there is no activity (Braun et al., 2003). The barrel and cork can be synthesized as separate polypeptide chains, and activity is still observed. The β-barrel is made first, and the cork is inserted later, extracytoplasmically (Braun et al., 2003). A single lipopolysaccharide is tightly associated with the transmembrane region of FhuA. Upon binding of ferrichrome-iron in an aromatic pocket near the cell surface, conformational changes are transduced to the periplasmic face of FhuA, signaling ligand-loading. Based on these findings, a structural model for TonB-dependent, FhuA-mediated siderophore-iron transport across the outer membrane of E. coli has been proposed. Substrate binding induces long-range structural changes that involve gating (Braun and Braun, 2002). Moreover, a ternary complex of FhuA, TonB and FhuD (the periplasmic ABC-type binding receptor) has been demonstrated (Carter et al., 2006). FhuD accepts ferrichrome from FhuA and passes it on to its ABC transporter. Some of these transporters are involved in siderophore-mediated signaling cascades that sense signals at the cell surface and control transcription of genes encoding proteins for siderophore transport and biosynthesis (Braun and Braun, 2002).
Three structures of the Serratia marcescens receptor, HasR (1.B.14.5.1) in complex with
its hemophore HasA, have been solved (Krieg et al., 2009). The transfer of heme over a distance of 9 Å from
its high-affinity site in HasA into a site of lower affinity in HasR is
coupled with the exergonic formation of the 2 protein complex. Upon
docking to the receptor, 1 of the 2 axial heme coordinations of the
hemophore is initially broken, but the position and orientation of the
heme is preserved. Subsequently, steric displacement of heme by a
receptor residue ruptures the other axial coordination, leading to heme
transfer into the receptor (Krieg et al., 2009).
OprC of Pseudomonas aeruginosa and NosA of P. stutzeri are two large outer membrane receptors that exhibit copper-binding (Kd = 2.6 µM), channel-forming, and Cu2+ transporting characteristics. Liposome swelling assays with the purified protein and planar bilayer ion conductance measurements suggested that OprC forms small channels after the precursor form (723 aas) is processed to the mature form (668 aas). NosA of P. stutzeri is 65% identical to OprC, and it conveys Cu2+ to intracellular acceptors. OprC synthesis is repressed by exogenous Cu2+ and derepressed by anaerobiosis in the presence of nitrate, results consistent with the conclusion that both it and NosA are involved in copper utilization.
Both one- and two-component TonB-dependent transport systems are known. Most OMRs are single-component systems and are analogous to the well-characterized siderophore receptors (TC #1.B.14.1.1-1.B.14.1.4 below). Two component systems consist of a TonB-dependent receptor homologous to those of the one component systems as well as an accessory lipoprotein. The HpuAB pair (TC #1.B.14.2.3) is one example of such a system, while the TbpAB (TC #1.B.14.2.12) and the LbpAB (TC #1.B.14.2.4) systems are two other examples. The LbpB and TbpB lipoproteins are homologous, but the smaller HpuA lipoprotein is not demonstrably homologous to either LbpB or TbpB.
The HasR receptors of Serratia marcescens and Pseudomonas aeruginosa use an extracellular processed haemophore, HasA, that captures free or haemoglobin-bound haem and shuttles it to HasR in preparation for transport across the outer membrane by a TonB-dependent mechanism. HasA is a monomeric protein that binds haem with very high affinity (Kd lower than 10-8 M) and binds HasR both in the heme-free and heme-loaded forms with a Kd of about 10-10 M. It is exported via an ABC-type export system. The iron-regulated iron-siderophore yersiniabactin receptors are also the pesticin receptors of Yersinia species which provide the entry route of the bacteriocin, pesticin.
Wolff et al. (2007) reported the 3-D NMR structure of apoHasA (TC# 1.A.14.5.1) and the backbone dynamics of both loaded and unloaded hemophore. While the overall structure of HasA is very similar in the apo and holo forms, the hemophore presents a transition from an open to a closed form upon ligand binding, through a large movement of up to 30 Å, of loop L1 bearing H32. Comparison of loaded and unloaded HasA dynamics on different time scales revealed striking flexibility changes in the binding pocket. These features provide the dual function of heme binding and release to the HasR receptor (Wolff et al., 2007).
The structure of the BtuB outer membrane receptor (OMR; 1.B.14.3.1) and the FhuA OMR (1.B.14.1.2) complexed with the C-terminal domain of TonB (2.C.1.1.1), the energy transmitter to the OMR from the ExbBD energizer, shows TonB binding to the TonB box in the OMRs. TonB binding causes the TonB box to form a β-strand, forming a β-sheet with TonB's own β-strand. This is consistent with a mechanical 'pulling' mechanism of transport (Shultis et al., 2006). The conserved TonB arginine 166 is oriented to form multiple contacts with the FhuA 'cork', the globublar domain enclosed by the β-barrel (Pawelek et al., 2006).
Transport results from energy-driven
movement of the TonB protein, which either pulls the plug out of the barrel
or causes it to rearrange within the barrel. Udho et al. (2009) discovered
that if the cis solution contains 4 M urea, then, with the periplasmic
side of the channel facing that solution, macroscopic conductances and
single channel events can be observed with FhuA, Cir, and BtuB. Channels generated by 4 M urea exposure were
not a consequence of general protein denaturation as their
ligand-binding properties were preserved. Thus, with FhuA, addition of
ferrichrome (its siderophore) to the trans, extracellular-facing side
reversibly inhibited 4 M urea-induced channel opening while blocking the
channel (Shultis et al., 2006). With Cir, addition of colicin Ia (the microbial toxin that
targets Cir) to the trans, extracellular-facing side, prevented 4 M
urea-induced channel opening. Maybe 4 M urea reversibly
unfolds the plugs, thereby opening an ion-conducting
pathway through these channels. This might mimic the
in vivo action of TonB on these plugs (Udho et al., 2009).
TonB-dependent transporters bind and transport ferric chelates, vitamin B12, nickel complexes, and carbohydrates. The transport process requires energy in the form of the pmf and the TonB-ExbB-ExbD complex to transduce this energy to the outer membrane. The siderophore substrates range in complexity from simple small molecules such as citrate to large proteins such as serum transferrin and hemoglobin. Expression can be regulated by metal-dependent regulators, σ/anti-σ factors, small RNAs, and a riboswitch (Noinaj et al., 2010). Noinaj et al. (2010) summarized the regulation, structure and function of these systems.
The generalized transport reaction for proteins of the OMR family is:
Substrate (out)  Substrate (periplasm)
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This family belongs to the Outer Membrane Pore-forming Protein I (OMPP-I) Superfamily .
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Nader, M., W. Dobbelaere, M. Vincent, L. Journet, H. Adams, D. Cobessi, J. Gallay, and I.J. Schalk. (2007). Identification of residues of FpvA involved in the different steps of Pvd-Fe uptake in Pseudomonas aeruginosa. Biochemistry 46: 11707-11717.
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Nau, C.D. and J. Konisky. (1989). Evolutionary relationship between the TonB-dependent outer membrane transport proteins: nucleotide and amino-acid sequences of the Escherichia coli colicin I receptor gene. J. Bacteriol. 171: 1041-1047.
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Oakhill, J.S., B.J. Sutton, A.R. Gorringe, and R.W. Evans. (2005). Homology modelling of transferrin-binding protein A from Neisseria meningitidis. Protein Eng Des Sel 18: 221-228.
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Obando S, T.A., M.M. Babykin, and V.V. Zinchenko. (2018). A Cluster of Five Genes Essential for the Utilization of Dihydroxamate Xenosiderophores in Synechocystis sp. PCC 6803. Curr. Microbiol. [Epub: Ahead of Print]
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Romagnoli, S., F. Agriesti, and V. Scarlato. (2011). In vivo recognition of the fecA3 target promoter by Helicobacter pylori NikR. J. Bacteriol. 193: 1131-1141.
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|
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.1.1 | FhuE ferric-coprogen receptor of 729 aas and 1 N-terminal TMS. It is required for the uptake of Fe3+ via coprogen, ferrioxamine B, and rhodotorulic acid (Hantke 1983). The crystal structure of FhuE in complex with coprogen was determined, providing a structural basis
to explain its selective promiscuity (Grinter and Lithgow 2019). The structural data, in
combination with functional analysis, showed that FhuE has evolved to specifically engage with planar siderophores. A
potential evolutionary driver, and a critical consequence of this
selectivity, is that it allows FhuE to exclude antibiotics that mimic nonplanar hydroxamate siderophores. These toxic molecules could otherwise cross the outer membrane barrier
through a Trojan horse mechanism (Grinter and Lithgow 2019). | Gram-negative bacteria | FhuE of E. coli |
| |
| 1.B.14.1.10 | The outer membrane ferrioxamine/desferrioxamine receptor, FoxA(1) (most like TC# 1.B.14.1.4 and 9) (Wei et al., 2007) | Bacteria | FoxA(1) of Nitrosomonas europaea (Q82VI7) |
| |
| 1.B.14.1.11 | The outer membrane ferric-anguibactin receptor/transporter, FatA (Lopez and Crosa, 2007) | Bacteria | FatA of Vibrio anguillarum (P11461) |
| |
| 1.B.14.1.12 | FecA ferric-citrate receptor (PA3901) (Marshall et al., 2009) (62% identical to the E. coli FecA).
| Gram-negative bacteria | FecA of Pseudomonas aeruginosa (Q9HXB2) |
| |
| 1.B.14.1.13 | CfrA ferric receptor (Carswell et al., 2008).
| Gram-negative bacteria | CfrA of Campylobacter jejuni (A3ZKG8) |
| |
| 1.B.14.1.14 | Ferric-pseudobactin 358 receptor | Bacteria | PupA of Pseudomonas putida |
| |
| 1.B.14.1.15 | Ferrichrome receptor FcuA | Bacteria | FcuA of Yersinia enterocolitica |
| |
| 1.B.14.1.16 | Probable TonB-dependent receptor BfrD (Virulence-associated outer membrane protein Vir-90) | Bacteria | BfrD of Bordetella pertussis |
| |
| 1.B.14.1.17 |
Ferrioxamine receptor, FoxA. Transports a variety of Ferrioxamine B analogues (Kornreich-Leshem et al. 2005). | Bacteria | FoxA of Yersinia enterocolitica |
| |
| 1.B.14.1.18 | TonB-dependent receptor (Bhat et al. 2011). | Proteobacteria | TonB-dependent receptor of Myxococcus xanthus |
| |
| 1.B.14.1.19 | TonB-dependent receptor | Proteobacteria | TonB-dependent receptor of Myxococcus xanthus |
| |
| 1.B.14.1.2 | FhuA ferrichrome (also albomycin and rifamycin; Colicin M; Microcin J25; Phage T5) receptor (transports phage T1, T5 and φ80 DNA across the outer membrane, dependent on DcrA (SdaC; TC #2.A.42.2.1) and DcrB) (Forms a complex with and acts with TonB and FhuD (the periplasmic binding receptor (3.A.1.14.3) to deliver siderophore to FhuD (Carter et al., 2006; Braun et al., 2009)). Deletion of the 160-residue cork domain and five large
extracellular loops converted this non-conductive, monomeric, 22-stranded beta-barrel
protein into a large-conductance protein pore (Wolfe et al. 2015). FhuA and its various applications indicate that it is a versatile building block to generate hybrid catalysts and materials (Sauer et al. 2023). | Gram-negative bacteria | FhuA of E. coli |
| |
| 1.B.14.1.20 | The iron-citrate receptor/transporter, FecA. TonB mediates both signaling and transport by unfolding portions of the transporter (Mokdad et al. 2012). The ferric citrate regulator, FecR, is translocated across the bacterial inner membrane via a unique Twin-arginine transport dependent mechanism (Passmore et al. 2020). | Bacteria | FecA of E. coli |
| |
| 1.B.14.1.21 | Ferrioxamine receptor | γ-Proteobacteria | Ferrioxamine receptor of Pseudovibrio sp. JE062 |
| |
| 1.B.14.1.22 | FepA ferri-enterobactin (also Colicins B and D) receptor for the 37 aas disulfide-containing K+ channel toxin, BgK (Braud et al., 2004). Functions by a "ball and chain" mechanism; The transport process involves expulsion of the N-terminal globular domain from the C-terminal beta-barrel (Ma et al. 2007). Conformational rearrangements occur in the N-terminus of FepA during FeEnt transport, but disengagement of the N-domain, out of the rigid channel suggests that it remains within the transmembrane pore as FeEnt enters the periplasm (Majumdar et al. 2020). | Gram-negative bacteria | FepA of E. coli |
| |
| 1.B.14.1.23 | OMR of 938 aas | Proteobacteria | OMR of Myxococcus xanthus |
| |
| 1.B.14.1.24 | Putative TonB-dependent siderophore receptor, Sde_3611 | Proteobacteria | Sde3611 of Saccharophagus degradans |
| |
| 1.B.14.1.25 | Nickel uptake receptor/channel of 724 aas (Benoit et al. 2013). | Proteobacteria | HH0418 of Helicobacter hepaticus |
| |
| 1.B.14.1.26 | Iron siderophore (ferripyoverdine) receptor and importer, FpvA of 808 aas (Ye et al. 2014). The crystal structure of FpvA has been solved at 3.6 Å resolution. It is folded in two domains: a transmembrane 22-stranded beta-barrel domain occluded by an N-terminal domain containing a mixed four-stranded beta-sheet (the plug). The beta-strands of the barrel are connected by long extracellular loops and short periplasmic turns (Cobessi et al. 2005). | Proteobacteria | FpvA of Pseudomonas aeruginosa |
| |
| 1.B.14.1.27 | Iron(III) dicitrate transport protein, FecA1: iron dicitrate uptake receptor of 767 aas. Regulated by the ferric uptake regulator transcription factor, Fur (van Vliet et al. 2002) in response to iron availability (Danielli et al. 2009). Involved in iron deficiency anemia in children (Kato et al. 2017). | | FecA1 of Helicobacter pylori |
| |
| 1.B.14.1.28 | FecA3 of 843 aas. Probable receptor for nickel. Shows 50% identiy with TC# 1.B.14.1.27. Repressed by nickel in the medium, mediated by NikR (Danielli et al. 2009). NikR seems to interact in an asymmetric mode with the fecA3 target to repress its transcription (Romagnoli et al. 2011). | | FecA3 of Helicobacter pylori |
| |
| 1.B.14.1.29 | Iron-deficiency-induced (2x) iron siderophore uptake outer membrane receptor, FhuA, of 828 aas and 1 N-terminal TMS (Qiu et al. 2018). | | FhuA of Synechocystis sp. (strain PCC 6803 / Kazusa) |
| |
| 1.B.14.1.3 | Ferric enterobactin (also ferricorynebactin) receptor, IroN | Gram-negative bacteria | IroN of Salmonella typhimurium |
| |
| 1.B.14.1.30 | Outer membrand iron siderophore uptake receptor of 853 aas and 1 N-terminal TMS, Slr1490. | | Slr1490 of Synechocystis sp. (strain PCC 6803 / Kazusa) |
| |
| 1.B.14.1.31 | Outer membrane porin, PiuA, of 753 aas. A deficiency of this iron transporter, PiuA in P. aeruginosa, caused 16-fold increases in cefiderocol resistance, suggesting that it contribute to the permeation of cefiderocol into the cell (Ito et al. 2018). | | PiuA of Pseudomonas aeruginosa |
| |
| 1.B.14.1.32 | Catechol iron-siderophore uptake system, IrgA, an iron-regulated outer membrane virulence protein, of 652 aas and 1 N-terminal TMS (Wyckoff et al. 2015). It is involved in the initial step of iron uptake by
binding ferric vibriobactin, an iron chelatin siderophore that allows
V. cholerae to extract iron from the environment and takes up linear enterobactin derivatives (Wyckoff et al. 2015).
| | IrgA of Vibrio cholerae |
| |
| 1.B.14.1.33 | Heme/hemin outer membrane TonB-related receptor of 708 aas, Tlr (Slakeski et al. 2000). | | Tlr of Porphyromonas gingivalis |
| |
| 1.B.14.1.4 | CirA Fe3+-catecholate receptor. Serves as the receptor for the TonB- and proton-dependent uptake of the E. coli bacteriocin, Microcin L (MccL) (Morin et al., 2011). CirA is also the translocator for colicin Ia (Jakes and Finkelstein, 2010). Plays roles in cefiderocol and ceftazidime resistance (Ito et al. 2018). Genotypic evolution of Klebsiella pneumoniae sequence type 512 during Ceftazidime/Avibactam, Meropenem/Vaborbactam,
and Cefiderocol treatment. This occurred through plasmid loss, outer membrane porin alteration, and a
nonsense mutation in the cirA siderophore gene, resulting in high levels
of cefiderocol resistance (Arcari et al. 2023). | Gram-negative bacteria | CirA of E. coli |
| |
| 1.B.14.1.5 | PfeA ferric enterobactin receptor | Gram-negative bacteria | PfeA of Pseudomonas aeruginosa |
| |
| 1.B.14.1.6 | Ferripyoverdine/pyocin S3 receptor, FpvA (Adams et al., 2006; Nader et al., 2007; Schalk et al., 2009; Nader et al., 2011) | Gram-negative bacteria | FpvA of Pseudomonas aeruginosa |
| |
| 1.B.14.1.7 | Iron malleobactin receptor, FmtA (Alice et al., 2006) | Gram-negative bacteria | FmtA of Burkholderia pseudomallei (EBA51007) |
| |
| 1.B.14.1.8 | The Ferripyochelin receptor, FptA (Michel et al., 2007). In addition to Fe3+, FptA takes up Co2+, Ga3+, and Ni2+ at low rates (Braud et al., 2009). The high resolution 3-d structure of FptA (2.0 Å) bound to iron-pyochelin has been solved (Cobessi et al. 2005). The pyochelin molecule provides atetra-dentate coordination of iron. The structure is typical of the TonB-dependent receptor/transporter superfamily. | Gram-negative bacteria | FptA of Pseudomonas aeruginosa (P42512) |
| |
| 1.B.14.1.9 | Ferric-catecholate siderophore (dihydroxybenzoylserine, dihydroxybenzoate) uptake receptor, Fiu or YbiL (Hantke, 1990; Curtis et al., 1988). Plays roles in cefiderocol and ceftazidime resistance (Ito et al. 2018). It can also transport catechol-substituted cephalosporins and is a receptor for microcins M, H47 and E492 (Patzer et al. 2003; Destoumieux-Garzón et al. 2006).
| Gram-negative bacteria | Fiu of E. coli (P75780) |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.10.1 | Heme/hemoglobin receptor, HmuR (also binds the Cu2+, Zn2+ and Fe2+ derivatives of protoporphyrin IX). Functions with the O.M. heme binding lipoprotein, HmuY (AAQ66587; Olczak et al., 2007). | Gram-negative bacteria | HmuR of Porphyromonas gingivalis |
| |
| 1.B.14.10.2 | TonB-dependent receptor | Proteobacteria | TonB receptor of Myxococcus xanthus |
| |
| 1.B.14.10.3 | TonB-dependent receptor | Proteobacteria | TonB recpetor of Myxocuccus xanthus |
| |
| 1.B.14.10.4 | Putative TonB-dependent receptor | Cyanobacteria | OMR of Gloeobacter violaceus |
| |
| 1.B.14.10.5 | Probable TonB-dependent long chain alkane receptor of 699 aas (Gregson et al. 2018). | | TonB-dependent receptor of Thalassolituus oleivorans |
| |
| 1.B.14.10.6 | Cobalt cation concentration sensitive Btu-like system, Btu1, of 698 aas and 1 N-terminal TMS. It facilitates cobalamin uptake in Anabaena sp. PCC 7120 (Graf et al. 2024). The regulation by cobalt and cobalamin as well as their uptakes are described for Anabaena sp. PCC 7120, a model filamentous heterocyst-forming cyanobacterium. Anabaena contains at least three cobalamin riboswitches in its genome, for one
of which the functionality was confirmed (Graf et al. 2024). Two outer
membrane-localized cobalamin TonB-dependent transporters, namely BtuB1
and BtuB2, were identified. BtuB2 is important for fast uptake of
cobalamin under conditions with low external cobalt, whereas BtuB1
appears to function in cobalamin uptake under conditions of sufficient
cobalt supply. While the general function is comparable, the specific
function of the two genes differs and mutants thereof show distinct
phenotypes. The uptake of cobalamin depends further on the TonB and a
BtuFCD machinery, as mutants of tonB3 and btuD show reduced cobalamin uptake rates. | | BtuB1 of Anabaena sp. PCC 7120 |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.11.1 | The Nickel (Ni2+) receptor (FrpB4; Hp1512) of 877 aas. Energized by the TonB/ExbBD complex (Schauer et al., 2007). Capable of binding both haem and haemoglobin but shows greater affinity for haem. The mRNA levels of frpB1 were repressed by iron and lightly modulated by haem or haemoglobin. Overexpression of the frpB1 gene supported cellular growth when haem or haemoglobin were supplied as the only iron source (Carrizo-Chávez et al. 2012). | Gram-negative bacteria | FrpB4 of Helicobacter pylori (Q9ZJA8) |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.12.1 | The TonB-dependent maltooligosaccharide OM receptor/porin, MalA (Lohmiller et al., 2008). | Bacteria | MalA of Caulobacter crescentus (Q9A608) |
| |
| 1.B.14.12.2 | The N-acetyl glucosamine/chitin oligosaccharide OM receptor porin, NagA (Eisenbeis et al., 2008). | Bacteria | NagA of Caulobacter crescentus (Q9AAZ6) |
| |
| 1.B.14.12.3 | TonB-dependent receptor | Proteobacteria | TonB-dependent receptor of Myxococcus xanthus |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.13.1 | TonB-dependent receptor of 763 aas | Proteobacteria | Receptor of Xanthomonas campestris |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.14.1 | The thiamine receptor (BT2390) (energized by TonB/ExbBD) (Rodionov et al. 2002). | Bacteroidetes | BT2390 of Bacteroides thetaiotaomicron (Q8A552) |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.15.1 | Putative porin of the DUF4289 family; 655 aas and 32 putative transmembrane beta strands. | Bacteroidetes | PP of Psychroflexus torquis |
| |
| 1.B.14.15.2 | Putative porin of 776 aas | Bacteroidetes | PP of Provotella ruminicola |
| |
| 1.B.14.15.3 | Putative porin of 631 aas | Bacteroidetes | PP of Amoebophilus asiaticus |
| |
| 1.B.14.15.4 | Putative DUF4289 family porin of 687 aas | Bacteroidetes | PP of Niastella koreensis |
| |
| 1.B.14.15.5 | Putative porin of 627 aas | Bacteroidetes | PP of Melioribacter roseus |
| |
| 1.B.14.15.6 | Putative porin of 650 aas | Ignavibacteriae | PP of Ignavibacterium album |
| |
| 1.B.14.15.7 | Putative porin of 621 aas | Bacteroidetes | PP of Cryptocercus punctulatus |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.16.1 | DUF940 homologue of 720 aas, one signal sequence and 30 putative β-strands. Homologous to proteins designated YmcA, WbfB and YjbH. | Chlamydiae | DUF940 homologue of Protochlamydia amoebophila |
| |
| 1.B.14.16.10 | Putative LPS exporter receptor, OtuG. It's gene is in a cluster with several LPS biosynthetic enzymes. | Proteobacteria | OtuG of Vibrio parahaemolyticus |
| |
| 1.B.14.16.11 | OMR of 698 aas and 1 N-terminal TMS, GlfD or YmcA. Probably involved in capsular polysaccharide export (Peleg et al. 2005). | | GlfD of E. coli |
| |
| 1.B.14.16.2 | DUF940 homologue of 953 aas, one N-terminal signal sequence and 30 putative beta strands. | Proteobacteria | DUF940 homologue of Chromobacterium violaceum |
| |
| 1.B.14.16.3 | DUF940 homologue of 689 aas, one N-terminal signal sequence and 28 putative TM β-strands. | Proteobacteria | DUF940 homologue of Psychromonas ingrahamii |
| |
| 1.B.14.16.4 | DUF940 homologue of 940 aas, one N-terminal signal sequence and 32 putative TM β-strands. | Proteobacteria | DUF940 homologue of E. coli |
| |
| 1.B.14.16.5 | DUF940 homologue of 716 aas with one N-terminal signal sequence and 27 putative beta strands. | Chlamydiae | DUF940 homologue of Parachlamydia acanthamoebae |
| |
| 1.B.14.16.6 | DUF940 homologue of 718 aas, an N-terminal signal sequence and 33 putative beta strands. | Proteobacteria | DUF940 homologue of Photobacterium angustum |
| |
| 1.B.14.16.7 | Putative polysaccharide exporter of 690 aas and 34 predicted TMSs, WbfB. Encoded in a gene cluster with polysaccharide biosynthetic enzymes and a putative periplasmic polysaccharide export protein. | Proteobacteria | Putative OMR concerned with polysaccharide export of Syntrophus aciditrophicus |
| |
| 1.B.14.16.8 | Putative polysaccharide/glycolipid/glycoprotein export receptor of 736 aas and 30 predicted β-strands, WbfB. The gene encoding this protein is in a cluster with UDP-N-acetyl D-quinovosamine -4 epimerase. | Proteobacteria | Putative exporter of Vibrio anguillarum |
| |
| 1.B.14.16.9 | Putative lipopolysaccharide export receptor, WbfB. It is encoded in a gene cluster with LPS biosynthetic genes. | Proteobacteria | WbfB of Vibrio parahaemolyticus |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.17.1 | Uncharacterized protein of 922 aas | Bacteroidetes | UP of Dyadobacter fermentans |
| |
| 1.B.14.17.2 | Putative Planctomycetes OMR of 799 aas | Planctomycetes | Putative OMR of Planctomyces brasiliensis |
| |
| 1.B.14.17.3 | Putative Planctomycetes OMR of 1101 aas | Planctomycetes | Putative OMR of Isosphaera pallida |
| |
| 1.B.14.17.4 | Uncharacterized protein of 1055 aas | Lentisphaerae | UP of Lentisphaera araneosa |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.18.1 | Putative Verucomicrobial OMP of 676 aas | Verucomicrobia | Putative OMR of Optutus terrae |
| |
| 1.B.14.18.2 | Uncharacterized OM channel superfamily member of 791 aas | Verrucomicrobia | UP of Pedosphaera parvula |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.19.1 | Putative TonB-dpenedent receptor of 790 aas, YddB. It is encoded by a gene adjacent to the YddA-encoding gene (TC# 3.A.1.203.11). YddA is a probable fatty acid exporter. the yddB gene is adjacent to a gene encoding a putative Zn2+ protease, PqqL. | | YddB of E. coli |
| |
| 1.B.14.19.2 | TonB-dependent receptor of 843 aas. | | Receptor of Rhodobacter capsulatus |
| |
| 1.B.14.19.3 | TonB-dependent receptor/transporter of 834 aas. | | Receptor of Verrucomicrobiaceae bacterium |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.2.1 | HmbR Hemoglobin receptor | Gram-negative bacteria | HmbR of Neisseria meningitidis |
| |
| 1.B.14.2.10 | Heme transporter BhuA (Brucella heme uptake protein A) | Bacteria | BhuA of Brucella abortus |
| |
| 1.B.14.2.11 | Heme/hemopexin utilization protein C | Bacteria | HxuC of Haemophilus influenzae |
| |
| 1.B.14.2.12 |
The transferrin receptor/lipoprotein complex, TbpAB (TbpA receptor, 912aas; TbpB lipoprotein, 625aas). The plug domain can fold independently of the beta-barrel, but extracellular loops of the beta-barrel are required for ferritin binding (Oke et al. 2004). | γ-Proteobacteria | TbpAB of Haemophilus influenzae
TbpA (P44970)
TbpB (P44971) |
| |
| 1.B.14.2.13 |
Hemoglobin receptor, HgbA. Residues for hemoglobin binding and utilization differ (Fusco et al. 2013). | Proteobacteria | HgbA of Haemophilus ducreyi |
| |
| 1.B.14.2.14 | Heme/hemoglobin receptor of 660 aas and 22 C-terminal β-strands with an N-terminal "plug" domain, ShuA. The 3-d structure is known to 2.6 Å resolution, revealing the histidyl residues in the barrel and plug that can interact with heme (Cobessi et al. 2010). | Proteobacteria | ShuA of Shigella dysenteriae |
| |
| 1.B.14.2.15 | Uncharacterized outer membrane receptor, probably for iron transport. | Proteobacteria | OMR of Xanthomonas oryzae |
| |
| 1.B.14.2.16 | Transferrin binding protein A, TbpA of 914 aas. A 3-D model revealed a narrow channel through the entire length of the protein. The spatial arrangement of external loops, and their relevance to the mechanism of iron translocation is presented (Oakhill et al. 2005). | | TbpA of Neisseria meningitidis |
| |
| 1.B.14.2.17 | The iron-catechol siderophore uptake/receptor, VctA, of 659 aas. Linear enterobactin derivatives are substrates, but it also transports the synthetic siderophore MECAM
[1,3,5-N,N',N″-tris-(2,3-dihydroxybenzoyl)-triaminomethylbenzene] (Wyckoff et al. 2015). | | VctA of Virbio cholerae |
| |
| 1.B.14.2.2 | HemR Heme (Hemin) receptor | Gram-negative bacteria | HemR of Yersinia enterocolitica |
| |
| 1.B.14.2.3 | HpuAB hemoglobin-haptoglobin receptor; porphyrin transporter (HpuA=lipoprotein; HpuB=OMR porin). Surface exposed loops in the gonococcal HpuB transporter are important for hemoglobin binding and utilization (Awate et al. 2023). | Gram-negative bacteria | HpuAB of Neisseria meningitidis |
| |
| 1.B.14.2.4 | Lactoferrin receptor (A=OMR porin; B=lipoprotein), LbpAB or IroAB. This two-component system extracts iron from the host glycoproteins lactoferrin and transferrin. Homologous iron-transport systems consist of a membrane-bound
transporter and an accessory lipoprotein. The
crystal structure of the N-terminal domain (N-lobe) of the accessory
lipoprotein, lactoferrin-binding protein B (LbpB) is homologous
to the structures of the accessory lipoproteins,
transferrin-binding protein B (TbpB) and LbpB from the bovine pathogen
Moraxella bovis. Docking the LbpB with lactoferrin reveals
extensive binding interactions with the N1 subdomain of lactoferrin. The
nature of the interaction precludes apolactoferrin from binding LbpB,
ensuring the specificity for iron-loaded lactoferrin, safeguarding proper delivery of iron-bound lactoferrin to the
transporter LbpA. The structure also
reveals a possible secondary role for LbpB in protecting the bacteria from host defences. Following
proteolytic digestion of lactoferrin, a cationic peptide derived from
the N-terminus is released. This peptide, called lactoferricin, exhibits
potent antimicrobial effects. The docked model of LbpB with lactoferrin
reveals that LbpB interacts extensively with the N-terminal
lactoferricin region (Brooks et al. 2014). | Gram-negative bacteria | LbpAB of Neisseria meningitidis |
| |
| 1.B.14.2.5 | TbpA single component transferrin receptor | Gram-negative bacteria | TbpA of Pasteurella multocida |
| |
| 1.B.14.2.6 | HugA heme receptor/porin
| Gram-negative bacteria | HugA of Plesiomonas shigelloides (Q93SS7) |
| |
| 1.B.14.2.7 | Hemin (Heme)-binding receptor, ShmR (also transports the toxic heme analog, gallium protoporphyrin) (Amarelle et al., 2008). | Bacteria | ShmR of Sinorhizobium meliloti (Q92N43) |
| |
| 1.B.14.2.8 | The heme-iron (from hemin and hemoglobin) utilization receptor, BhuR (Brickman et al., 2006; Vanderpool and Armstrong, 2004). | Gram-negative bacteria | BhuR of Bordetella pertussis (Q7VSQ4) |
| |
| 1.B.14.2.9 | Probable TonB-dependent receptor NMB0964 | | Y964 of Neisseria meningitidis MC58 |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.3.1 | BtuB cobalamin receptor (also transports phage C1 DNA across the outer membrane). Two Ca2+ binding sites in BtuB mediate cobalamine binding (Cadieux et al., 2007). Cobalamine uptake into the periplasm is reversible, but efflux is pmf-independent (Cadieux et al., 2007). The 3-d structure is available (PDB#1NQE). The Ton box and the
extracellular substrate binding site are allosterically coupled (bidirectional), and TonB binding may
initiate a partial round of transport (Sikora et al. 2016). Substrate binding to the extracellular surface of the protein triggers the unfolding of an energy
coupling motif at the periplasmic surface. Thus, substrate binding reduces the interaction free
energy between certain residues, thereby triggering the unfolding of the energy coupling motif (Lukasik et al. 2007). Multiple extracellular loops contribute to substrate binding and transport by BtuB (Fuller-Schaefer and Kadner 2005). | Gram-negative bacteria | BtuB of E. coli |
| |
| 1.B.14.3.2 | TonB-dependent receptor (Bhat et al. 2011). | Proteobacteria | TonB-dependent receptor of Myxococcus xanthus |
| |
| 1.B.14.3.3 | TonB-dependent receptor (Bhat et al. 2011). | Proteobacteria | TonB receptor of Myxococcus xanthus |
| |
| 1.B.14.3.4 | TonB-dependent receptor (Bhat et al. 2011). | Proteobacteria | TonB-dependent receptor of Myxococcus xanthus |
| |
| 1.B.14.3.5 | TonB-dependent receptor (Bhat et al. 2011). | Proteobacteria | TonB-dependent receptor of Myxococcus xanthus |
| |
| 1.B.14.3.6 | Probable siderophore-specific outer membrane receptor of 869 aas, MxcH | Proteobacteria | MxcH of Stigmatella aurantiaca |
| |
| 1.B.14.3.7 | TonB-dependent receptor | Proteobacteria | OMR of Shewanella oneidensis |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.4.1 | Cu2+-transporting, Cu2+-regulated outer membrane protein C, OprC (Yoneyama and Nakae 1996). OprC impairs host defense by increasing the quorum-sensing-mediated virulence of P. aeruginosa (Gao et al. 2020). | Gram-negative bacteria | OprC of Pseudomonas aeruginosa |
| |
| 1.B.14.4.2 | Cu2+-transporting, outer membrane protein, NosA | Gram-negative bacteria | NosA of Pseudomonas stutzeri |
| |
| 1.B.14.4.3 | TonB-dependent receptor/channel for substrate uptake across the outer membrane of 656 aas | | Receptor of E. coli |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.5.1 | HasR receptor-HasA haemophore heme receptor complex (HasA, an extracellular heme binding protein, binds one heme and transfers it directly to HasR, which uses HasB (2.C.1.1.2) (a TonB homologue) instead of TonB (2.C.1.1.1) for energization) (Benevides-Matos et al., 2008; Izadi-Pruneyre et al., 2006; Lefèvre et al., 2008; Benevides-Matos and Biville, 2010). A signaling domain in HasR interacts with a partially unfolded periplasmic domain of an antisigma factor, HasS, to control transcription by an ECF sigma factor (Malki et al. 2014). The
HasR domain responsible for signal transfer is highly flexible in two stages of signaling,
extends into the periplasm at about 70 to 90 A from the HasR beta-barrel and exhibits local
conformational changes in response to the arrival of signaling activators (Wojtowicz et al. 2016). Studies revealed a previously unidentified network of HasR-HasB protein-protein interactions in the periplasm (Somboon et al. 2024). | Gram-negative bacteria | HasR-HasA of Serratia marcescens |
| |
| 1.B.14.5.2 | The heme receptor HxuC (PA1302) serves as a pyocin M4 (Colicin M-type; PaeM4) target at the cellular surface. | | HxuC of Pseudomonas aeruginosa |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.6.1 | SusC receptor/porin for maltooligosaccharides (up to maltoheptaose). Forms a complex with and functions with SusD porin (TC# 8.A.46.1.1) as well as SusE and SusF porins (TC#s 1.B.38.1.1 and 1.2) as well as the SusG α-amylase (TC#8.A.9.1.3). These proteins are all involved in starch utilization (Shipman et al. 2000; Reeves et al. 1997; Cho and Salyers 2001; Foley et al. 2018). | Gram-negative bacteria | SusC of Bacteroides thetaiotaomicron |
| |
| 1.B.14.6.10 | DUF4480 putative OMR of 835 aas. | Bacteroidetes | OMR of Capnocytophaga canimorsus |
| |
| 1.B.14.6.11 | OMR (DUF4480) of 976 aas | Bacteroidetes | OMR of Zobellia galactanivorans |
| |
| 1.B.14.6.12 | OMR (DUF4480) of 775 aas | Bacteroidetes | OMR of Saprospira grandis |
| |
| 1.B.14.6.13 | SusC homologue of 940 aas. Functions with SusD homolgoue TC# 8.A.46.1.2. | Bacteroidetes | SusC homologue of Bacteroides thetaiotaomicron |
| |
| 1.B.14.6.14 | Putative porin of 830 aas and 16 predicted TMSs. The β-barrel domain is the N-terminal ~250 aas which corresponds to the DUF4480 or Peptidase M14NE family in Pfam. The large hydrophilic C-terminal domain is of unknown function. | Bacteroidetes | Putative porin of Aequorivita sublithincola |
| |
| 1.B.14.6.15 | TonB-dependent collagenase (proteinase) of 1047 aas (Bhattacharya et al. 2017). The primary pathogen of the Great Barrier Reef sponge, Rhopaloeides odorabile, identified as a unique strain (NW4327) of Pseudoalteromonas agarivorans. It produces collagenases which degrade R. odorabile skeletal fibers. | | Collagenase of Pseudoalteromonas agarivolans NW4327 (a marine sponge parasite) |
| |
| 1.B.14.6.16 | Possible Iron receptor, RagA of 1036 aas. Its gene forms part of a small operon which may have arisen via horizontal
gene transfer into the genome. The 55 kDa antigen (RagB; TC# 8.A.46.3.5), encoded within the same operon, may act in concert at the surface of the bacterium to
facilitate active transport, mediated through the periplasmic spanning protein, TonB (Curtis et al. 1999). | | RagAB of Porphyromonas gingivalis |
| |
| 1.B.14.6.17 | SusC of 1041 aas and 1 N-terminal TMS (Joglekar et al. 2018). | | SusC of Bacteroides thetaiotaomicron |
| |
| 1.B.14.6.18 | TonB-dependent receptor/transporter of 909 aas | | Receptor of Granulicella mallensis |
| |
| 1.B.14.6.2 | The Omp200 porin complex (consists of Omp121 [an OMR family member] and Omp71 [a protein nonhomologous to other proteins in the databases]) | Gram-negative bacteria | Omp121/Omp71 complex of Bacteroides fragilis |
| |
| 1.B.14.6.3 | Outer membrane porin required for intercellular signalling via C-signal (CsgA), Oar (Bhat et al. 2011). | Proteobacteria | Oar of Myxococcus xanthus |
| |
| 1.B.14.6.4 | TonB-dependent outer membrane porin/receptor, Oar | Proteobacteria | Oar of Stenotrophomonas maltophila |
| |
| 1.B.14.6.5 | TonB-dependent outer membrane receptor of 792 aas. | Bacteroidetes | TonB receptor of Bacteroides caccae |
| |
| 1.B.14.6.6 | TonB-dependent receptor of 970 aas | Spirochaetes | TonB receptor of Leptospira interrogans |
| |
| 1.B.14.6.7 | TonB-dependent receptor | Bacteroidetes | TonB receptor of Pedobacter heparinus |
| |
| 1.B.14.6.8 | Putative OMR (DUF4480) of 709 aas and one N-terminal TMS. The first 120 residues show sequence similarity with TC#1.B.14.6.2. | Bacteroidetes | Putative OMR of Bacteroides fragilis |
| |
| 1.B.14.6.9 | Putative OMR (DUF4480) of 828 aas, and N-terminal TMS and 32 predicted TM β-strands. | Bacteroidetes | Putative OMR of Croceibacter atlanticus |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.7.1 | CjrC outer membrane receptor of 753 aas. It is iron and temperature regulated, and functions with CjrB, a distant TonB homologue (TC# 2.C.1.1.3). Together these two proteins are required for uptake of colicin J in Shigella and enteroinvasive E. coli strains (Smajs and Weinstock 2001). | Proteobacteria | CjrC of E. coli |
| |
| 1.B.14.7.2 | Probable TonB-dependent receptor NMB1497 | Bacteria | NMB1497 of Neisseria meningitidis |
| |
| 1.B.14.7.3 | Probable TonB-dependent receptor HI_1217 | Bacteria | HI_1217 of Haemophilus influenzae |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.8.1 | Putative salicin/arbutin (aromatic β-glucoside) receptor, SalC | Gram-negative bacteria | SalC of Azospirillum irakense |
| |
| 1.B.14.8.2 | The iron (Fe3+) · pyridine-2,6-bis(thiocarboxylic acid) (PDTC) receptor, PdtK. Functions with the MFS carrier, PdtE (TC #2.A.1.55.1) (Leach and Lewis, 2006). | Gram-negative bacteria | PdtK of Pseudomonas putida (ABC68350) |
| |
| 1.B.14.8.3 | Vibriobactin receptor, VuiA or VuuA of 687 aas and 1 N-terminal TMS. There is conserved, global coordinate iron regulation in V. cholerae by the Fur transcription factor, responsive to iron (Butterton et al. 1992). V. cholerae synthesizes and uses the catechol siderophore vibriobactin and also uses siderophores secreted by other species, including enterobactin produced by E. coli (Wyckoff et al. 2015). ViuB, a putative V. cholerae siderophore-interacting protein (SIP),
functionally substituted for the E. coli ferric reductase YqjH, which
promotes the release of iron from the siderophore in the bacterial
cytoplasm. In V. cholerae, ViuB is required for the use of vibriobactin but is not required for the use of MECAM, fluvibactin, ferrichrome, or the linear derivatives of enterobactin, all substrates of ViuA (Wyckoff et al. 2015). | Bacteria | ViuA of Vibrio cholerae serotype O1 |
| |
| 1.B.14.8.4 | The thiamine receptor (SO2715) (energized by TonB/ExbBD) (Rodionov et al. 2002) | Proteobacteria | SO2715 of Shewanella oneidensis (Q8EDM8) |
| |
| 1.B.14.8.5 | TonB-dependent receptor of 726 aas. | Proteobacteria | Receptor of Colwellia psychrerythraea |
| |
| 1.B.14.8.6 | The (thio)quinolobactin receptor, QbsI, of 669 aa | Proteobacteria | QbsI of Pseudomonas fluorescens |
| |
| 1.B.14.8.7 | FyuA Fe3+-yersiniabactin and pesticin (Psn; a bacteriocin) receptor and uptake protein of 673 aas. It contributes to biofilm formation and infection (Hancock et al., 2008). It is similar to FrpA, an outer membrane protein involved in piscibactin secretion in Vibrio anguillarum (Lages et al. 2022). | Gram-negative bacteria | FyuA of Yersinia enterocolitica (P0C2M9) |
| |
| Examples: |
| TC# | Name | Organismal Type | Example |
| 1.B.14.9.1 | RhtA Rhizobactin 1021 (siderophore) receptor/porin | Gram-negative bacteria | RhtA of Sinorhizobium meliloti |
| |
| 1.B.14.9.2 | Acr ferric achromobactin (hydroxycarboxylate siderophore) receptor/porin (Franza et al., 2005) | Gram-negative bacteria | Acr of Erwinia chrysanthemi (AAL14566) |
| |
| 1.B.14.9.3 |
The ferric ferrichrome/aerobactin receptor/porin, IutA (Forman et al., 2007) | Bacteria | IutA of Yersinia pestis (Q7CGN6) |
| |
| 1.B.14.9.4 | Putative TonB-dependent heme receptor | Proteobacteria | TonB-dependent heme receptor of Campylobacter jejuni |
| |
| 1.B.14.9.5 | TonB-dependent receptor of 700 aas, YncD, a probable iron transporter/receptor in the outer membrane. Deletion of the orthologous yncD genes in Salmonella strains leads to attenuated strains, potentially useful for vaccine development (Xiong et al. 2012; Xiong et al. 2015). Its synthesis is depressed by inclusion of high glucose concentrations in the medium (Yang et al. 2011). YncD is a receptor for a T1-like Escherichia coli phage named vB_EcoS_IME347 (IME347) (Li et al. 2018). | | YncD of E. coli |
| |
| 1.B.14.9.6 | SchT (IutA) is capable of using dihydroxamate xenosiderophores, either ferric schizokinen (FeSK) or a siderophore of the filamentous cyanobacterium Anabaena variabilis ATCC 29413 (SAV), as the sole source of iron in a TonB-dependent manner (Obando S et al. 2018). Functions with the ABC uptake system having the TC# 3.A.1.14.24. | | SchT of Synechocystis sp. PCC 6803 |
| |