Summary: POT family
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This is the Wikipedia entry entitled "Proton-dependent oligopeptide transporter". More...
Proton-dependent oligopeptide transporter Edit Wikipedia article
| POT family | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | PTR2 | ||||||||
| Pfam | PF00854 | ||||||||
| InterPro | IPR000109 | ||||||||
| PROSITE | PDOC00784 | ||||||||
| TCDB | 2.A.17 | ||||||||
| OPM superfamily | 15 | ||||||||
| OPM protein | 2xut | ||||||||
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Proteins of the Proton-dependent Oligopeptide Transporter (POT) Family (also called the PTR (peptide transport) family) are found in animals, plants, yeast, archaea and both Gram-negative and Gram-positive bacteria, and are part of the major facilitator superfamily. The transport of peptides into cells is a well-documented biological phenomenon which is accomplished by specific, energy-dependent transporters found in a number of organisms as diverse as bacteria and humans. The proton-dependent oligopeptide transporter (PTR) family of proteins is distinct from the ABC-type peptide transporters and was uncovered by sequence analyses of a number of recently discovered peptide transport proteins.[1] These proteins that seem to be mainly involved in the intake of small peptides with the concomitant uptake of a proton.[2]
Contents
Function
While most members of the POT family catalyze peptide transport, one is a nitrate permease and one can transport histidine, as well as peptides. Some of the peptide transporters can also transport antibiotics. They function by proton symport, but the substrate:H+ stoichiometry is variable: the high-affinity rat PepT2 carrier catalyzes uptake of 2 and 3 H+ with neutral and anionic dipeptides, respectively, while the low affinity PepT1 carrier catalyzes uptake of one H+ per neutral peptide.[3][4]
Transport Reaction
The generalized transport reaction catalyzed by the proteins of the POT family is:
substrate (out) + H (out) → substrate (in) H+ (in)
Structure and Mechanism
The proteins are of about 450-600 amino acyl residues in length with the eukaryotic proteins in general being longer than the bacterial proteins. They exhibit 12 putative or established transmembrane α-helical spanners.
Pairs of salt bridge interactions between transmembrane helices work in tandem to orchestrate alternating access transport within the PTR family.[5] Key roles for residues conserved between bacterial and eukaryotic homologues suggest a conserved mechanism of peptide recognition and transport that in some cases has been subtly modified in individual species.
Subfamilies
- Oligopeptide transporter, peptide:H+ symporter InterPro: IPR004768
- Amino acid/peptide transporter InterPro: IPR005279
Human proteins containing this domain
FP12591; PEPT1; PTR4; SLC15A1; SLC15A2; SLC15A3; SLC15A4; hPEPT1-RF;
References
- ^ Naider F, Becker JM, Steiner HY (1995). "The PTR family: a new group of peptide transporters". Mol. Microbiol. 16 (5): 825–834. doi:10.1111/j.1365-2958.1995.tb02310.x. PMID 7476181.
- ^ Skurray RA, Paulsen IT (1994). "The POT family of transport proteins". Trends Biochem. Sci. 19 (10): 404–404. doi:10.1016/0968-0004(94)90087-6. PMID 7817396.
- ^ Bucking, Carol; Schulte, Patricia M. (2012-04-01). "Environmental and nutritional regulation of expression and function of two peptide transporter (PepT1) isoforms in a euryhaline teleost". Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology. 161 (4): 379–387. doi:10.1016/j.cbpa.2011.12.008. ISSN 1531-4332. PMID 22227314.
- ^ Chen, Xing-Zhen (29 Jan 1999). "Stoichiometry and kinetics of the high-affinity H+-coupled peptide transporter PepT2". Journal of Biological Chemistry. 274 (5). doi:10.1074/jbc.274.5.2773. PMID 9915809.
- ^ Doki, Shintaro; Kato, Hideaki E.; Solcan, Nicolae; Iwaki, Masayo; Koyama, Michio; Hattori, Motoyuki; Iwase, Norihiko; Tsukazaki, Tomoya; Sugita, Yuji (2013-07-09). "Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT". Proceedings of the National Academy of Sciences of the United States of America. 110 (28): 11343–11348. doi:10.1073/pnas.1301079110. ISSN 1091-6490. PMC 3710879. PMID 23798427.
As of this edit, this article uses content from "2.A.17 The Proton-dependent Oligopeptide Transporter (POT/PTR) Family", which is licensed in a way that permits reuse under the Creative Commons Attribution-ShareAlike 3.0 Unported License, but not under the GFDL. All relevant terms must be followed.
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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.
POT family Provide feedback
The POT (proton-dependent oligopeptide transport) family all appear to be proton dependent transporters [1].
Literature references
-
Paulsen IT, Skurray RA; , Trends Biochem Sci 1994;19:404-404.: The POT family of transport proteins. PUBMED:7817396 EPMC:7817396
Internal database links
| SCOOP: | BT1 DUF3784 DUF4397 MFS_1 MFS_1_like MFS_2 MFS_3 MFS_4 OATP Sugar_tr TRI12 |
| Similarity to PfamA using HHSearch: | Sugar_tr MFS_1 |
External database links
| PROSITE: | PDOC00784 |
| Transporter classification: | 2.A.17 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR000109
The proton-dependent oligopeptide transporter (POT) family (also known as the peptide transport (PTR) family) is made up of a group of energy-dependent transporters found in organisms as diverse as bacteria and humans. The POT family of proteins is distinct from the ABC-type peptide transporters and was uncovered by sequence analyses of peptide transport proteins [ PUBMED:7476181 ]. They seem to be mainly involved in the intake of small peptides [ PUBMED:7817396 ]. However, some family members are nitrate permeases and others are involved in histidine transport [ PUBMED:17481610 ].
Gene Ontology
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) |
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 MFS (CL0015), which has the following description:
The major facilitator superfamily (MFS) is one of the two largest families of membrane transporters found on Earth [1]. It is present ubiquitously in bacteria, archaea, and eukarya and includes members that can function by solute uniport, solute/cation symport, solute/cation antiport and/or solute/solute antiport with inwardly and/or outwardly directed polarity [1]. All permeases of the MFS possess either 12 or 14 transmembrane helices [1].
The clan contains the following 23 members:
Acatn ATG22 BT1 Folate_carrier FPN1 LacY_symp MFS_1 MFS_1_like MFS_2 MFS_3 MFS_4 MFS_5 MFS_Mycoplasma Nodulin-like Nuc_H_symport Nucleoside_tran OATP PTR2 PUCC Sugar_tr TLC TRI12 UNC-93Alignments
We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...
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| Seed (21) |
Full (28124) |
Representative proteomes | UniProt (70336) |
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| RP15 (3067) |
RP35 (12622) |
RP55 (23928) |
RP75 (36027) |
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| PP/heatmap | 1 | ||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
| Seed (21) |
Full (28124) |
Representative proteomes | UniProt (70336) |
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|---|---|---|---|---|---|---|---|
| RP15 (3067) |
RP35 (12622) |
RP55 (23928) |
RP75 (36027) |
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| Raw Stockholm | |||||||
| Gzipped | |||||||
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
Trees
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.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
Curation
| Seed source: | Pfam-B_571 (release 3.0) |
| Previous IDs: | none |
| Type: | Family |
| Sequence Ontology: | SO:0100021 |
| Author: |
Bateman A 
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| Number in seed: | 21 |
| Number in full: | 28124 |
| Average length of the domain: | 320.70 aa |
| Average identity of full alignment: | 20 % |
| Average coverage of the sequence by the domain: | 70.58 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 397 | ||||||||||||
| Family (HMM) version: | 23 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
Archea
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Eukaryota
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Viruses
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Unclassified sequence
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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 PTR2 domain has been found. There are 76 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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