Summary: Toxin Fst, type I toxin-antitoxin system

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Wikipedia: Par stability determinant
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This is the Wikipedia entry entitled "Par stability determinant". More...

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Par stability determinant Edit Wikipedia article

RNAII

Secondary structure of RNAII
Identifiers
Symbol	fstAT
Rfam	RF01797
Other data
RNA type	Gene; antitoxin
Domain(s)	Enterococcus faecalis

Fst Type I toxin-antitoxin system

Identifiers

Symbol

Fst_toxin

Pfam

PF13955

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

The par stability determinant is a 400 bp locus of the pAD1 plasmid which encodes a type I toxin-antitoxin system in Enterococcus faecalis.^[1]^[2] It was the first such plasmid addiction module to be found in gram-positive bacteria.^[3]

The par locus contains two genes: fst which encodes a 33-amino acid toxic protein and a gene for RNAII, the small RNA anti-toxin which inhibits fst translation.^[4] The two genes are found on opposite DNA strands and share a 5' region which is where they are thought to have an antisense interaction.^[4] Their RNA secondary structures have been predicted computationally, the complementary regions appear to be presented on exposed loops for interaction.^[4]

par maintains pAD1 by means of post-segregational killing (PSK). If a daughter cell does not inherit the par locus, the unstable RNAII will quickly degrade leaving the long-lived fst toxin to damage or kill the daughter cell.^[5]

References [edit]

^ Weaver KE, Walz KD, Heine MS (November 1998). "Isolation of a derivative of Escherichia coli-Enterococcus faecalis shuttle vector pAM401 temperature sensitive for maintenance in E. faecalis and its use in evaluating the mechanism of pAD1 par-dependent plasmid stabilization". Plasmid 40 (3): 225â32. doi:10.1006/plas.1998.1368. PMID 9806859. |accessdate= requires |url= (help)
^ Weaver KE, Jensen KD, Colwell A, Sriram SI (April 1996). "Functional analysis of the Enterococcus faecalis plasmid pAD1-encoded stability determinant par". Mol. Microbiol. 20 (1): 53â63. doi:10.1111/j.1365-2958.1996.tb02488.x. PMID 8861204. |accessdate= requires |url= (help)
^ Shokeen S, Greenfield TJ, Ehli EA, Rasmussen J, Perrault BE, Weaver KE (March 2009). "An intramolecular upstream helix ensures the stability of a toxin-encoding RNA in Enterococcus faecalis". J. Bacteriol. 191 (5): 1528â36. doi:10.1128/JB.01316-08. PMC 2648210. PMID 19103923. Retrieved 2010-09-20.
^ ^a ^b ^c Greenfield TJ, Ehli E, Kirshenmann T, Franch T, Gerdes K, Weaver KE (August 2000). "The antisense RNA of the par locus of pAD1 regulates the expression of a 33-amino-acid toxic peptide by an unusual mechanism". Mol. Microbiol. 37 (3): 652â60. doi:10.1046/j.1365-2958.2000.02035.x. PMID 10931358. Retrieved 2010-09-20.
^ Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND (1997). "Antisense RNA-regulated programmed cell death". Annu. Rev. Genet. 31: 1â31. doi:10.1146/annurev.genet.31.1.1. PMID 9442888. |accessdate= requires |url= (help)

External links [edit]

Page for fst antitoxin sRNA (RNAII) at Rfam

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.

Toxin Fst, type I toxin-antitoxin system Provide feedback

Fst (faecalis plasmid stabilization toxin), also known as RNA I, is a toxic peptide. Its N-terminus forms a transmembrane alpha helix, its C terminus is disordered and is likely to be cytosolic. Its translation is inhibited by the antisense RNA, RNA II, which acts as an antitoxin [1,2].

Literature references

Greenfield TJ, Weaver KE;, Mol Microbiol. 2000;37:661-670.: Antisense RNA regulation of the pAD1 par post-segregational killing system requires interaction at the 5' and 3' ends of the RNAs. PUBMED:10931359 EPMC:10931359
Gobl C, Kosol S, Stockner T, Ruckert HM, Zangger K;, Biochemistry. 2010;49:6567-6575.: Solution structure and membrane binding of the toxin fst of the par addiction module. PUBMED:20677831 EPMC:20677831

External database links

PANDIT:	PF13955
Pseudofam:	PF13955
SYSTERS:	Fst_toxin

This tab holds annotation information from the InterPro database.

InterPro entry IPR025882

Fst (faecalis plasmid stabilisation toxin), also known as RNA I, is a toxic peptide. Its N terminus forms a transmembrane alpha helix, its C terminus is disordered and is likely to be cytosolic. Its translation is inhibited by the antisense RNA, RNA II, which acts as an antitoxin [PUBMED:10931359, PUBMED:20677831].

Domain organisation

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Alignments

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There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.

Alignment types

We make a range of alignments for each Pfam-A family:

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full: the alignment generated by searching the sequence database using the HMM
RP15/RP35/RP55/RP75: Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
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meta: alignment generated by searching the metagenomics sequence database using the family HMM

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You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.

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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 (13)	Full (45)	Representative proteomes				NCBI (25)	Meta (0)
	Seed (13)	Full (45)	RP15 (0)	RP35 (1)	RP55 (2)	RP75 (5)	NCBI (25)	Meta (0)
Jalview	View	View		View	View	View	View
HTML	View	View		View	View	View
PP/heatmap	₁	View		View	View	View
Pfam viewer	View	View

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

Key: available, not generated, — not available.

Format an alignment

	Seed (13)	Full (45)	Representative proteomes				NCBI (25)	Meta (0)
	Seed (13)	Full (45)	RP15 (0)	RP35 (1)	RP55 (2)	RP75 (5)	NCBI (25)	Meta (0)
Alignment:
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

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 (13)	Full (45)	Representative proteomes				NCBI (25)	Meta (0)
	Seed (13)	Full (45)	RP15 (0)	RP35 (1)	RP55 (2)	RP75 (5)	NCBI (25)	Meta (0)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

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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:

Jackhmmer:Q9RLG7

Previous IDs:

none

Type:

Domain

Author:

Eberhardt R

Number in seed:

13

Number in full:

45

Average length of the domain:

21.00 aa

Average identity of full alignment:

62 %

Average coverage of the sequence by the domain:

62.92 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	36.0	36.0
Trusted cut-off	36.2	36.3
Noise cut-off	31.9	35.7

Model length:

21

Family (HMM) version:

1

Download:

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Species distribution

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How the sunburst is generated

The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.

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Unmapped species names

The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.

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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.

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Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

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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 Fst_toxin domain has been found. There are 1 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 seqence.

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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: Fst_toxin (PF13955)

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