Summary: Formate/nitrite transporter
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Formate-nitrite transporter Edit Wikipedia article
The Formate-Nitrite Transporter (FNT) Family belongs to the Major Intrinsic Protein (MIP) Superfamily. FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea, yeast, plants and lower eukaryotes. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.
With the exception of the yeast protein (627 amino acyl residues), all characterized members of the family are of 256-285 residues in length and exhibit 6-8 putative transmembrane Î±-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. The yeast protein has a similar apparent topology but has a large C-terminal hydrophilic extension of about 400 residues.
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.
The energy coupling mechanisms for proteins of the FNT family have not been extensively characterized. HCOâˆ’
2 and NOâˆ’
2 uptakes may be coupled to H+ symport. HCOâˆ’
2 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.
FocA, transports short-chain acids. 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. 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.
The probable transport reactions catalyzed by different members of the FNT family are:
2 or NOâˆ’
2 (out) â‡Œ RCOâˆ’
2 or NOâˆ’
2 (in) â‡Œ HCOâˆ’
(3) HSâˆ’ (out) â‡Œ HSâˆ’ (in).
A representative 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).
- Reizer J, Reizer A, Saier MH (1993-01-01). "The MIP family of integral membrane channel proteins: sequence comparisons, evolutionary relationships, reconstructed pathway of evolution, and proposed functional differentiation of the two repeated halves of the proteins". Critical Reviews in Biochemistry and Molecular Biology. 28 (3): 235â€“57. doi:10.3109/10409239309086796. PMIDÂ 8325040.
- Park JH, Saier MH (October 1996). "Phylogenetic characterization of the MIP family of transmembrane channel proteins". The Journal of Membrane Biology. 153 (3): 171â€“80. doi:10.1007/s002329900120. PMIDÂ 8849412. S2CIDÂ 1559932.
- 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". Molecular Microbiology. 11 (5): 965â€“82. doi:10.1111/j.1365-2958.1994.tb00375.x. PMIDÂ 8022272. S2CIDÂ 6425651.
- Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu YN, Wang P, Yan N, Shi Y (November 2009). "Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel". Nature. 462 (7272): 467â€“72. Bibcode:2009Natur.462..467W. doi:10.1038/nature08610. PMIDÂ 19940917. S2CIDÂ 4370839.
- Saier, MH Jr. "1.A.16 The Formate-Nitrite Transporter (FNT) Family". Transporter Classification Database. Saier Lab Bioinformatics Group / SDSC.
- Falke D, Schulz K, Doberenz C, Beyer L, Lilie H, Thiemer B, Sawers RG (February 2010). "Unexpected oligomeric structure of the FocA formate channel of Escherichia coliÂ : a paradigm for the formate-nitrite transporter family of integral membrane proteins". FEMS Microbiology Letters. 303 (1): 69â€“75. doi:10.1111/j.1574-6968.2009.01862.x. PMIDÂ 20041954.
- LÃ¼ W, Du J, Wacker T, Gerbig-Smentek E, Andrade SL, Einsle O (April 2011). "pH-dependent gating in a FocA formate channel". Science. 332 (6027): 352â€“4. Bibcode:2011Sci...332..352L. doi:10.1126/science.1199098. PMIDÂ 21493860. S2CIDÂ 20059830.
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Formate/nitrite transporter Provide feedback
Proteins in this entry belong to the Formate-Nitrite Transporter (FNT) family and includes the nitrite transport protein NirC and formate channel FocA [1,2]. They have a pentameric architecture with structural similarity to aquaporins and glyceroporins . Proteins in this family transport the structurally related compounds, formate and nitrite.
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External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000292
Proteins in this entry belong to the Formate-Nitrite Transporter (FNT) family (TC 2.A.44). The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite. The homologous yeast protein may function as a short chain aliphatic carboxylate H+ symporter, transporting formate, acetate and propionate, and functioning primarily as an acetate uptake permease.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||membrane (GO:0016020)|
|Molecular function||transmembrane transporter activity (GO:0022857)|
|Biological process||transmembrane transport (GO:0055085)|
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This clan groups families with an aquaporin-like structure comprising the canonical right-handed bundle of 6 transmembrane (TM) alpha-helices from aquaporins [1,2,3].
The clan contains the following 3 members:Form_Nir_trans MIP SpecificRecomb
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|Author:||Finn RD , Bateman A|
|Number in seed:||484|
|Number in full:||5017|
|Average length of the domain:||239.90 aa|
|Average identity of full alignment:||26 %|
|Average coverage of the sequence by the domain:||81.74 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||20|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Form_Nir_trans domain has been found. There are 110 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.