Formate-nitrite transporter
| Form_Nir_trans | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | Form_Nir_trans | ||||||||
| Pfam | PF01226 | ||||||||
| InterPro | IPR000292 | ||||||||
| PROSITE | PDOC00769 | ||||||||
| TCDB | 2.A.44 | ||||||||
| OPM superfamily | 7 | ||||||||
| OPM protein | 3tdp | ||||||||
| |||||||||
The Formate-Nitrite Transporter (FNT) Family (TC# 1.A.16) are a family of homologous transmembrane proteins. The FNT family is a member of the Major Intrinsic Protein (MIP) Superfamily. FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea and yeast. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.[1]
Structure
With the exception of the yeast protein (627 amino acyl residues), all members of the family are of 256-285 residues in length and exhibit 6-8 putative transmembrane α-helical spanners (TMSs). In one case, that of the E. coli FocA (TC# 1.A.16.1.1) protein, a 6 TMS topology has been established. Wang et al. (2009) reported the crystal structure of the E. coli FocA at 2.25 Å resolution.[2] The yeast protein has a similar apparent topology but has a large C-terminal hydrophilic extension of about 400 residues.
FocA of E. coli has a pentameric quaternary structure. FocA forms a symmetric pentamer, with each protomer consisting of six TMSs. Despite a lack of sequence homology, the overall structure of the FocA protomer closely resembles that of aquaporin, indicating that FocA is a channel rather than a carrier. Structural analysis identified potentially important channel residues, defined the channel path and revealed two constriction sites. Unlike aquaporin, FocA is impermeable to water but allows the passage of formate.
Phylogeny
The phylogenetic tree shows clustering according to function and organismal phylogeny. The putative formate efflux transporters (FocA; TC#s 1.A.16.1.1 and 1.A.16.1.3) of bacteria associated with pyruvate-formate lyase (pfl) comprise cluster I; the putative formate uptake permeases (FdhC; TC#s 1.A.16.2.1 and 1.A.16.2.3) of bacteria and archaea associated with formate dehydrogenase comprise cluster II; the nitrite uptake permeases (NirC, TC#s 1.A.16.2.5, 1.A.16.3.1, and 1.A.16.3.4) of bacteria comprise cluster III, and a yeast protein comprises cluster IV.[3]
Function
The energy coupling mechanisms for proteins of the FNT family have not been extensively characterized. HCO2- and NO2- uptakes are probably coupled to H+ symport. HCO2- efflux may be driven by the membrane potential by a uniport mechanism or by H+ antiport. FocA of E. coli catalyzes bidirectional formate transport and may function by a channel-type mechanism.[4]
FocA, a representative member of the formate-nitrite transporter family, transports short-chain acids in bacteria, archaea, fungi, algae and certain eukaryotic parasites. FocA may be able to switch its mode of operation from a passive export channel at high external pH to a secondary active formate/H importer at low pH. The crystal structure of Salmonella typhimurium FocA at pH 4.0 shows that this switch involves a major rearrangement of the amino termini of individual protomers in the pentameric channel.[5] The amino-terminal helices open or block transport in a concerted, cooperative action that indicates how FocA is gated in a pH-dependent way. Electrophysiological studies show that the protein acts as a specific formate channel at pH 7.0 and that it closes upon a shift of pH to 5.1.
Transport Reaction
The probable transport reactions catalyzed by different members of the FNT family are:
(1) RCO2- or NO2- (out) ⇌ RCO2- or NO2- (in),
(2) HCO2- (in) ⇌ HCO2- (out),
(3) HS- (out) ⇌ HS- (in).
Members
A list of the currently classified members belonging to the FNT family can be found in the Transporter Classification Database. Some characterized members include:
- FocA and FocB (TC#s 1.A.16.1.1 and 1.A.16.1.2, respectively), from Escherichia coli, transporters involved in the bidirectional transport of formate.
- FdhC, from Methanobacterium maripaludis (TC# 1.A.16.2.3) and Methanothermobacter thermoformicicum (TC# 1.A.16.2.1), a probable formate transporter.
- NirC, from E. coli (TC# 1.A.16.3.1), a probable nitrite transporter.
- Nar1 (TC# 1.A.16.2.4) of Chlamydomonas reinhardtii (Chlamydomonas smithii), a nitrite uptake porter of 355 amino acyl residues.
- B. subtilis hypothetical protein YwcJ (ipa-48R) (TC# 1.A.16.3.2).
References
- ↑ Suppmann B, Sawers G (March 1994). "Isolation and characterization of hypophosphite--resistant mutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter". Mol. Microbiol. 11 (5): 965–82. doi:10.1111/j.1365-2958.1994.tb00375.x. PMID 8022272.
- ↑ Wang, Yi; Huang, Yongjian; Wang, Jiawei; Cheng, Chao; Huang, Weijiao; Lu, Peilong; Xu, Ya-Nan; Wang, Pengye; Yan, Nieng (2009-11-26). "Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel". Nature 462 (7272): 467–472. doi:10.1038/nature08610. ISSN 1476-4687. PMID 19940917.
- ↑ Saier, MH Jr. "1.A.16 The Formate-Nitrite Transporter (FNT) Family". Transporter Classification Database. Saier Lab Bioinformatics Group / SDSC.
- ↑ Falke, Dörte; Schulz, Kristin; Doberenz, Claudia; Beyer, Lydia; Lilie, Hauke; Thiemer, Barbara; Sawers, Robert Gary (2010-02-01). "Unexpected oligomeric structure of the FocA formate channel of Escherichia coli : a paradigm for the formate-nitrite transporter family of integral membrane proteins". FEMS microbiology letters 303 (1): 69–75. doi:10.1111/j.1574-6968.2009.01862.x. ISSN 1574-6968. PMID 20041954.
- ↑ Lü, Wei; Du, Juan; Wacker, Tobias; Gerbig-Smentek, Elke; Andrade, Susana L. A.; Einsle, Oliver (2011-04-15). "pH-dependent gating in a FocA formate channel". Science (New York, N.Y.) 332 (6027): 352–354. doi:10.1126/science.1199098. ISSN 1095-9203. PMID 21493860.
This article incorporates text from the public domain Pfam and InterPro IPR000292