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110  structures 3270  species 0  interactions 5017  sequences 47  architectures

Family: Form_Nir_trans (PF01226)

Summary: Formate/nitrite transporter

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This is the Wikipedia entry entitled "Formate-nitrite transporter". More...

Formate-nitrite transporter Edit Wikipedia article

Form_Nir_trans
Identifiers
SymbolForm_Nir_trans
PfamPF01226
InterProIPR000292
PROSITEPDOC00769
TCDB2.A.44
OPM superfamily7
OPM protein3tdp

The Formate-Nitrite Transporter (FNT) Family belongs to the Major Intrinsic Protein (MIP) Superfamily.[1][2] 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.[3]

Structure

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 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.[4] The yeast protein has a similar apparent topology but has a large C-terminal hydrophilic extension of about 400 residues.

FocA of E. coli is a symmetric pentamer, with each subunit consisting of six TMSs.[4]

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.[5]

Function

The energy coupling mechanisms for proteins of the FNT family have not been extensively characterized. HCO−
2
and NO−
2
uptakes may be coupled to H+ symport. HCO−
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.[6]

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.[7] 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) RCO−
2
or NO−
2
(out) ⇌ RCO−
2
or NO−
2
(in),

(2) HCO−
2
(in) ⇌ HCO−
2
(out),

(3) HS− (out) ⇌ HS− (in).

Members

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).

References

  1. ^ 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): 235–57. doi:10.3109/10409239309086796. PMID 8325040.
  2. ^ Park JH, Saier MH (October 1996). "Phylogenetic characterization of the MIP family of transmembrane channel proteins". The Journal of Membrane Biology. 153 (3): 171–80. doi:10.1007/s002329900120. PMID 8849412. S2CID 1559932.
  3. ^ 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): 965–82. doi:10.1111/j.1365-2958.1994.tb00375.x. PMID 8022272. S2CID 6425651.
  4. ^ a b 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): 467–72. Bibcode:2009Natur.462..467W. doi:10.1038/nature08610. PMID 19940917. S2CID 4370839.
  5. ^ Saier, MH Jr. "1.A.16 The Formate-Nitrite Transporter (FNT) Family". Transporter Classification Database. Saier Lab Bioinformatics Group / SDSC.
  6. ^ 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 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. PMID 20041954.
  7. ^ Lü 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): 352–4. Bibcode:2011Sci...332..352L. doi:10.1126/science.1199098. PMID 21493860. S2CID 20059830.
This article incorporates text from the public domain Pfam and InterPro: IPR000292

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

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 [1]. Proteins in this family transport the structurally related compounds, formate and nitrite.

Literature references

  1. Czyzewski BK, Wang DN;, Nature. 2012;483:494-497.: Identification and characterization of a bacterial hydrosulphide ion channel. PUBMED:22407320 EPMC:22407320


Internal database links

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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Aquaporin-like (CL0716), which has the following description:

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

Alignments

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(484)
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(669)
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(2394)
RP55
(4923)
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(8881)
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  Seed
(484)
Full
(5017)
Representative proteomes UniProt
(25101)
RP15
(669)
RP35
(2394)
RP55
(4923)
RP75
(8881)
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  Seed
(484)
Full
(5017)
Representative proteomes UniProt
(25101)
RP15
(669)
RP35
(2394)
RP55
(4923)
RP75
(8881)
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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Prosite
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 34.6 34.6
Trusted cut-off 35.1 34.6
Noise cut-off 34.3 34.2
Model length: 236
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

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Structures

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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