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0  structures 5284  species 0  interactions 23774  sequences 16  architectures

Family: LysE (PF01810)

Summary: LysE type translocator

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Homoserine/threonine resistance transporter". More...

Homoserine/threonine resistance transporter Edit Wikipedia article

Homoserine lactone efflux protein
Identifiers
SymbolRhtB
PfamPF01810
InterProIPR004778.

The resistance to homoserine/threonine (RhtB) family (TC# 2.A.76) belongs to the lysine exporter (LysE) superfamily of transporters.[1] Hundreds of sequenced proteins, derived from Gram-negative and Gram-positive bacteria as well as archaea, comprise the RhtB family, but few of these proteins are functionally characterized.[2]

Members

The first two members of the RhtB family to be characterized functionally were the RhtB (TC# 2.A.76.1.1) and RhtC (TC# 2.A.76.1.2) permeases of E. coli.[3][4]

E. coli possesses five paralogues, and a large region of one of them (YahN of E. coli; TC# 2.A.76.1.3) exhibits significant sequence similarity to YggA of E. coli (TC# 2.A.75.1.2), an established member of the LysE family (TC #2.A.75).

The PSI-BLAST program groups the LysE family (TC# 2.A.75), the RhtB family and the CadD family (TC #2.A.77) together. These proteins are all of about the same size and apparent topology, further suggesting a common evolutionary origin.[2]

The leucine exporter homologue (YeaS or LeuE; TC# 2.A.76.1.5) exports leucine and several other neutral, hydrophobic amino acids.[5]

A representative list of proteins belonging to the RhtB family can be found in the Transporter Classification Database.

General transport reaction

The transport reaction presumably catalyzed by members of the RhtB family is:[6]

amino acid (in) + nH+ (out) ⇌ amino acid (out) + nH+ (in)

See also

References

  1. ^ Tsu BV, Saier MH (2015-01-01). "The LysE Superfamily of Transport Proteins Involved in Cell Physiology and Pathogenesis". PLOS ONE. 10 (10): e0137184. Bibcode:2015PLoSO..1037184T. doi:10.1371/journal.pone.0137184. PMC 4608589. PMID 26474485.
  2. ^ a b Vrljic M, Garg J, Bellmann A, Wachi S, Freudl R, Malecki MJ, Sahm H, Kozina VJ, Eggeling L, Saier MH, Eggeling L, Saier MH (November 1999). "The LysE superfamily: topology of the lysine exporter LysE of Corynebacterium glutamicum, a paradyme for a novel superfamily of transmembrane solute translocators". Journal of Molecular Microbiology and Biotechnology. 1 (2): 327–36. PMID 10943564.
  3. ^ Aleshin VV, Zakataeva NP, Livshits VA (April 1999). "A new family of amino-acid-efflux proteins". Trends in Biochemical Sciences. 24 (4): 133–5. doi:10.1016/s0968-0004(99)01367-5. PMID 10322417.
  4. ^ Zakataeva NP, Aleshin VV, Tokmakova IL, Troshin PV, Livshits VA (June 1999). "The novel transmembrane Escherichia coli proteins involved in the amino acid efflux". FEBS Letters. 452 (3): 228–32. doi:10.1016/s0014-5793(99)00625-0. PMID 10386596. S2CID 11107959.
  5. ^ Kutukova EA, Livshits VA, Altman IP, Ptitsyn LR, Zyiatdinov MH, Tokmakova IL, Zakataeva NP (August 2005). "The yeaS (leuE) gene of Escherichia coli encodes an exporter of leucine, and the Lrp protein regulates its expression". FEBS Letters. 579 (21): 4629–34. doi:10.1016/j.febslet.2005.07.031. PMID 16098526. S2CID 31930231.
  6. ^ "TCDB » SEARCH". www.tcdb.org. Retrieved 2016-02-25.

As of 25 February 2016, this article is derived in whole or in part from Transporter Classification Database, authored by Saier Lab Bioinformatics. The copyright holder has licensed the content in a manner that permits reuse under CC BY-SA 3.0 and GFDL. All relevant terms must be followed. The original text was at "2.A.76 The Resistance to Homoserine/Threonine (RhtB) Family"


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

This is the Wikipedia entry entitled "Lysine exporter". More...

Lysine exporter Edit Wikipedia article

D- and L-lysine, histidine and arginine exporter (LysE)
Identifiers
SymbolLysE aka CGL1262
PfamPF01810
InterProIPR001123
TCDB2.A.75
OPM superfamily248
OPM protein2n4x

Lysine Exporters are a superfamily of transmembrane proteins [1][2] which export amino acids, lipids and heavy metal ions.[2] They provide ionic homeostasis, play a role in cell envelope assembly, and protect from excessive concentrations of heavy metals in cytoplasm. The superfamily was named based on the early discovery of the LysE carrier protein of Corynebacterium glutamicum.

Families

2.A.75 - The L-Lysine Exporter (LysE) Family

2.A.76 - The Resistance to Homoserine/Threonine (RhtB) Family

2.A.77 - The Cadmium Resistance (CadD) Family

2.A.95 - The 6TMS Neutral Amino Acid Transporter (NAAT) Family

2.A.106 - The Ca2+:H+ Antiporter-2 (CaCA2) Family

2.A.107 - The Mn2+ exporter (MntP) Family

2.A.108 - The Iron/Lead Transporter (ILT) Family

2.A.109 - The Tellurium Ion Resistance (TerC) Family

2.A.113 - The Nickel/Cobalt Transporter (NicO) Family

2.A.116 - The Peptidoglycolipid Addressing Protein (GAP) Family

5.A.1 - The Disulfide Bond Oxidoreductase D (DsbD) Family

The LysE family

Two members of the LysE family (LysE of Corynebacterium glutamicum (TC# 2.A.75.1.1) and ArgO of E. coli) have been functionally characterized, but functionally uncharacterized homologues are encoded within the genomes of many bacteria including Bacillus subtilis, Mycobacterium tuberculosis, Aeromonas salmonicida, Helicobacter pylori, Vibrio cholerae and Yersinia pestis. Thus, LysE family members are found widely distributed in Gram-negative and Gram-positive bacteria.

Structure

These proteins are 190-240 amino acyl residues in length and possess six hydrophobic regions. PhoA fusion analyses of LysE of C. glutamicum provided evidence for a 5 transmembrane α-helical spanner (TMS) typology with the N-terminus inside and the C-terminus outside.[3] However, some evidence suggests a 6 TMS topology.[4]

Function

LysE appears to catalyze unidirectional efflux of L-lysine (and other basic amino acids such as L-arginine), and it provides the sole route for L-lysine excretion. The energy source is believed to be the proton motive force (H+ antiport). The E. coli ArgO homologue (TC# 2.A.75.1.2) effluxes arginine and possibly lysine and canavanine as well.[5]

Early studies showed that the LysE family is related to the RhtB family (TC #2.A.76) as well as the CadD family (TC #2.A.77) based both on the similar sizes and topologies of their members and on PSI-BLAST results.[3]

Generalized Transport Reaction

The generalized transport reaction for LysE is:

Lysine (in) + [nH+ (out) or nOH− (in)] Lysine (out) + [nH+ (in) or nOH− (out)].

References

 This article incorporates text available under the CC BY 4.0 license.

  1. ^ Vrljic M, Garg J, Bellmann A, Wachi S, Freudl R, Malecki MJ, Sahm H, Kozina VJ, Eggeling L, Saier MH, Eggeling L, Saier MH (November 1999). "The LysE superfamily: topology of the lysine exporter LysE of Corynebacterium glutamicum, a paradyme for a novel superfamily of transmembrane solute translocators". Journal of Molecular Microbiology and Biotechnology. 1 (2): 327–36. PMID 10943564.
  2. ^ a b Tsu BV, Saier MH (2015-01-01). "The LysE Superfamily of Transport Proteins Involved in Cell Physiology and Pathogenesis". PLOS ONE. 10 (10): e0137184. Bibcode:2015PLoSO..1037184T. doi:10.1371/journal.pone.0137184. PMC 4608589. PMID 26474485.
  3. ^ a b Vrljic M, Sahm H, Eggeling L (December 1996). "A new type of transporter with a new type of cellular function: L-lysine export from Corynebacterium glutamicum". Molecular Microbiology. 22 (5): 815–26. doi:10.1046/j.1365-2958.1996.01527.x. PMID 8971704. S2CID 26112791.
  4. ^ Saier, MH Jr. "2.A.75 The L-Lysine Exporter (LysE) Family". Transporter Classification Database. Saier Lab Bioinformatics Group / SDSC.
  5. ^ Nandineni MR, Gowrishankar J (June 2004). "Evidence for an arginine exporter encoded by yggA (argO) that is regulated by the LysR-type transcriptional regulator ArgP in Escherichia coli". Journal of Bacteriology. 186 (11): 3539–46. doi:10.1128/JB.186.11.3539-3546.2004. PMC 415761. PMID 15150242.

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.

LysE type translocator Provide feedback

This family consists of various hypothetical proteins and an l-lysine exporter LysE P94633 from Corynebacterium glutamicum which is proposed to be the first of a novel family of translocators [1]. LysE exports l-lysine from the cell into the surrounding medium and is predicted to span the membrane six times [1]. The physiological function of the exporter is to excrete excess l-Lysine as a result of natural flux imbalances or peptide hydrolysis; and also after artificial deregulation of l-Lysine biosynthesis as used by the biotechnology. industry for the production of l-lysine [1].

Literature references

  1. Vrljic M, Sahm H, Eggeling L; , Mol Microbiol 1996;22:815-826.: A new type of transporter with a new type of cellular function: L- lysine export from Corynebacterium glutamicum. PUBMED:8971704 EPMC:8971704

  2. Aleshin VV, Zakataeva NP, Livshits VA; , Trends Biochem Sci 1999;24:133-135.: A new family of amino-acid-efflux proteins. PUBMED:10322417 EPMC:10322417


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001123

A number of amino acid exporter proteins belong to this family. LeuE encodes an exporter of leucine and some other structurally unrelated amino acids [ PUBMED:16098526 ]. This family also includes threonine efflux protein RhtC [ PUBMED:10386596 ], arginine exporter protein ArgO/YggA [ PUBMED:15150242 ], as well as a number of uncharacterised proteins from a variety of sources.

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 LysE (CL0292), which has the following description:

This clan includes a diverse range of transporter families [1].

The clan contains the following 19 members:

BacA Cad Colicin_V DsbD DsbD_2 DUF475 DUF6044 FTR1 HupE_UreJ HupE_UreJ_2 LysE MarC Mntp NicO OFeT_1 SfLAP TauE TerC UPF0016

Alignments

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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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(16)
Full
(23774)
Representative proteomes UniProt
(138364)
RP15
(1879)
RP35
(9448)
RP55
(24849)
RP75
(50816)
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PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(16)
Full
(23774)
Representative proteomes UniProt
(138364)
RP15
(1879)
RP35
(9448)
RP55
(24849)
RP75
(50816)
Alignment:
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Sequence:
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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
(16)
Full
(23774)
Representative proteomes UniProt
(138364)
RP15
(1879)
RP35
(9448)
RP55
(24849)
RP75
(50816)
Raw Stockholm Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download    

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 View help on the curation process

Seed source: Pfam-B_1537 (release 4.2) & Pfam-B_7916 (Release 8.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bashton M , Bateman A
Number in seed: 16
Number in full: 23774
Average length of the domain: 189.90 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 91.68 %

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 25.6 25.6
Trusted cut-off 25.6 25.6
Noise cut-off 25.5 25.5
Model length: 193
Family (HMM) version: 21
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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.

Protein Predicted structure External Information
A6T515 View 3D Structure Click here
A6T7N0 View 3D Structure Click here
A6TDS8 View 3D Structure Click here
A8AHJ0 View 3D Structure Click here
O05406 View 3D Structure Click here
O06730 View 3D Structure Click here
O53528 View 3D Structure Click here
O87005 View 3D Structure Click here
P0AG34 View 3D Structure Click here
P0AG36 View 3D Structure Click here
P0AG37 View 3D Structure Click here
P0AG38 View 3D Structure Click here
P0AG39 View 3D Structure Click here
P11667 View 3D Structure Click here
P38101 View 3D Structure Click here
P38102 View 3D Structure Click here
P74343 View 3D Structure Click here
P75693 View 3D Structure Click here
P76249 View 3D Structure Click here
P94381 View 3D Structure Click here
P94633 View 3D Structure Click here
P9WK31 View 3D Structure Click here
P9WK33 View 3D Structure Click here
Q2G1T0 View 3D Structure Click here
Q32FT6 View 3D Structure Click here
Q57320 View 3D Structure Click here
Q6D090 View 3D Structure Click here
Q6NHP1 View 3D Structure Click here
Q7CQP8 View 3D Structure Click here
Q7N183 View 3D Structure Click here
Q7UBP8 View 3D Structure Click here
Q83K22 View 3D Structure Click here
Q8RQM4 View 3D Structure Click here
Q8XA19 View 3D Structure Click here
Q8XD10 View 3D Structure Click here
Q8XDS6 View 3D Structure Click here
Q8ZHH6 View 3D Structure Click here
Q8ZM68 View 3D Structure Click here
Q8ZMX5 View 3D Structure Click here
Q9KVK7 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;