Summary: Piwi domain

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Wikipedia: Argonaute
Wikipedia: Piwi
Pfam
InterPro

This is the Wikipedia entry entitled "Argonaute". More...

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Argonaute Edit Wikipedia article

An argonaute protein from Pyrococcus furiosus.

Argonaute proteins are the catalytic components of the RNA-induced silencing complex (RISC), the protein complex responsible for the gene silencing phenomenon known as RNA interference (RNAi). Argonaute proteins bind small interfering RNA (siRNA) fragments and have endonuclease activity directed against messenger RNA (mRNA) strands that are complementary to their bound siRNA fragment. The proteins are also responsible for selection of the guide strand and destruction of the passenger strand of the siRNA substrate.^[1]

The proteins have been identified in high concentrations in regions of the cell's cytoplasm known as cytoplasmic bodies, to which mRNA decay is also localized.^[2]

References

^ Rand TA, Petersen S, Du F, Wang X. (2005). Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation. Cell 123(4):621-9.
^ Sen GL, Blau HM. (2005). Argonaute 2/RISC resides in sites of mammalian mRNA decay known as cytoplasmic bodies. Nat Cell Biol 7(6):633-6.

This protein-related article is a stub. You can help Wikipedia by expanding it.

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 "Piwi". More...

The Wikipedia text that you see displayed here is a download from Wikipedia. This means that the information we display is a copy of the information from the Wikipedia database. The button next to the article title ("Edit Wikipedia article") takes you to the edit page for the article directly within Wikipedia. You should be aware you are not editing our local copy of this information. Any changes that you make to the Wikipedia article will not be displayed here until we next download the article from Wikipedia. We currently download new content on a nightly basis.

Does Pfam agree with the content of the Wikipedia entry ?

Pfam has chosen to link families to Wikipedia articles. In some case we have created or edited these articles but in many other cases we have not made any direct contribution to the content of the article. The Wikipedia community does monitor edits to try to ensure that (a) the quality of article annotation increases, and (b) vandalism is very quickly dealt with. However, we would like to emphasise that Pfam does not curate the Wikipedia entries and we cannot guarantee the accuracy of the information on the Wikipedia page.

Editing Wikipedia articles

Before you edit for the first time

Wikipedia is a free, online encyclopedia. Although anyone can edit or contribute to an article, Wikipedia has some strong editing guidelines and policies, which promote the Wikipedia standard of style and etiquette. Your edits and contributions are more likely to be accepted (and remain) if they are in accordance with this policy.

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How your contribution will be recorded

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If you have problems editing a particular page, contact us at pfam-help@sanger.ac.uk and we will try to help.

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Piwi Edit Wikipedia article

The piwi domain of an argonaute protein with bound siRNA, components of the RNA-induced silencing complex that mediates gene silencing by RNA interference.

The piwi (sometimes also PIWI) class of genes was originally identified as encoding regulatory proteins responsible for maintaining incomplete differentiation in stem cells and maintaining the stability of cell division rates in germ line cells.^[1] Piwi proteins are highly conserved across evolutionary lineages and are present in both plants and animals.^[2] One of the major human homologs, whose upregulation is implicated in the formation of tumors such as seminomas, is called hiwi.^[3]

The piwi domain is a protein domain homologous to piwi proteins and present in a large number of nucleic acid-binding proteins, especially those that bind and cleave RNA. The best-studied such family of proteins is the argonaute family; argonautes are RNase H-like enzymes that carry out the catalytic functions of the RNA-induced silencing complex (RISC). In the well-known cellular process of RNA interference, the argonaute protein in the RISC complex binds siRNA or miRNA molecules generated by the ribonuclease dicer, and cleaves complementary base pairing messenger RNA, destroying it and preventing its translation into a protein. Crystallized piwi domains have a conserved basic binding site for the 5' end of bound RNA; in the case of argonaute proteins binding siRNA strands, the last unpaired nucleotide base of the siRNA is also stabilized by base stacking interactions between the base and neighboring tyrosine residues.^[4]

References

^ Cox DN, Chao A, Lin H. (2000). piwi encodes a nucleoplasmic factor whose activity modulates the number and division rate of germline stem cells. Development 127(3):503-14. PMID 10631171
^ Cox DN, Chao A, Baker J, Chang L, Qiao D, Lin H. (1998). A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev 12(23):3715-27. PMID 9851978
^ Qiao D, Zeeman AM, Deng W, Looijenga LH, Lin H. (2002). Molecular characterization of hiwi, a human member of the piwi gene family whose overexpression is correlated to seminomas. Oncogene 21(25):3988-99. PMID 12037681
^ Ma J, Yuan Y, Meister G, Pei Y, Tuschl T, Patel D (2005). "Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein". Nature 434 (7033): 666-70. PMID 15800629

External links

SCOP PIWI domain family

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.

Piwi domain Provide feedback

This domain is found in the protein Piwi and its relatives. The function of this domain is the dsRNA guided hydrolysis of ssRNA. Determination of the crystal structure of Argonaute reveals that PIWI is an RNase H domain, and identifies Argonaute as Slicer, the enzyme that cleaves mRNA in the RNAi RISC complex [2]. In addition, Mg+2 dependence and production of 3'-OH and 5' phosphate products are shared characteristics of RNaseH and RISC. The PIWI domain core has a tertiary structure belonging to the RNase H family of enzymes. RNase H fold proteins all have a five-stranded mixed beta-sheet surrounded by helices. By analogy to RNase H enzymes which cleave single-stranded RNA guided by the DNA strand in an RNA/DNA hybrid, the PIWI domain can be inferred to cleave single-stranded RNA, for example mRNA, guided by double stranded siRNA.

Literature references

Cerutti L, Mian N, Bateman A; , Trends Biochem Sci 2000;25:481-482.: Domains in gene silencing and cell differentiation proteins: the novel PAZ domain and redefinition of the Piwi domain. PUBMED:11050429 EPMC:11050429
Song JJ, Smith SK, Hannon GJ, Joshua-Tor L; , Science 2004;305:1434-1437.: Crystal structure of Argonaute and its implications for RISC slicer activity. PUBMED:15284453 EPMC:15284453

Internal database links

SCOOP:

ArgoMid

This tab holds annotation information from the InterPro database.

InterPro entry IPR003165

The piwi domain [ PUBMED:11050429 ] is a protein domain found in piwi proteins and a large number of related nucleic acid-binding proteins, especially those that bind and cleave RNA. The function of the domain is double stranded-RNA-guided hydrolysis of single stranded-RNA, as has been determined in the argonaute family of related proteins [ PUBMED:15284453 ].

Gene Ontology

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

Molecular function

nucleic acid binding (GO:0003676)

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 RNase_H (CL0219), which has the following description:

This clan includes a diverse set of nucleases that share a similar structure to Ribonuclease H.

The clan contains the following 70 members:

Arena_ncap_C CAF1 DDE_1 DDE_2 DDE_3 DDE_5 DDE_Tnp_1 DDE_Tnp_1_2 DDE_Tnp_1_3 DDE_Tnp_1_4 DDE_Tnp_1_5 DDE_Tnp_1_6 DDE_Tnp_1_7 DDE_Tnp_2 DDE_Tnp_4 DDE_Tnp_IS1 DDE_Tnp_IS1595 DDE_Tnp_IS240 DDE_Tnp_IS66 DDE_Tnp_ISAZ013 DDE_Tnp_ISL3 DDE_Tnp_Tn3 Dimer_Tnp_Tn5 DNA_pol_A_exo1 DNA_pol_B_exo1 DNA_pol_B_exo2 DNA_pol_P_Exo DUF1258 DUF2779 DUF3882 DUF3892 DUF4152 DUF99 Endonuclease_5 KDZ Maelstrom Methyltransf_1N MGMT_N MULE NurA OrfB_IS605 Piwi Plant_tran Plavaka Pox_A22 Ribosomal_S30AE RNase_H RNase_H_2 RNase_HII RNase_T RNaseH_like RT_RNaseH RT_RNaseH_2 RuvC RuvC_1 Rv2179c-like rve rve_2 rve_3 RVT_3 Taq-exonuc TerL_nuclease Terminase_3C Terminase_6C Transposase_1 Transposase_21 Transposase_mut UPF0236 UvrC_RNaseH_dom Ydc2-catalyt

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...

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:

seed: the curated alignment from which the HMM for the family is built
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
UniProt: alignment generated by searching the UniProtKB sequence database using the family HMM

Viewing

You can see the alignments as HTML or in three different sequence viewers:

jalview: a Java applet developed at the University of Dundee. You will need Java installed before running jalview
HTML: an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
PP/Heatmap: an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.

Reformatting

You can download (or view in your browser) a text representation of a Pfam alignment in various formats:

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You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.

Downloading

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.

View options

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 (15)	Full (14038)	Representative proteomes				UniProt (22300)
	Seed (15)	Full (14038)	RP15 (2628)	RP35 (6003)	RP55 (11131)	RP75 (14647)	UniProt (22300)
Jalview	View	View	View	View	View	View	View
HTML	View
PP/heatmap	₁

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

Key: available, not generated, — not available.

Format an alignment

	Seed (15)	Full (14038)	Representative proteomes				UniProt (22300)
	Seed (15)	Full (14038)	RP15 (2628)	RP35 (6003)	RP55 (11131)	RP75 (14647)	UniProt (22300)
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 (15)	Full (14038)	Representative proteomes				UniProt (22300)
	Seed (15)	Full (14038)	RP15 (2628)	RP35 (6003)	RP55 (11131)	RP75 (14647)	UniProt (22300)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download
Gzipped	Download	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

Seed source:

Bateman A

Previous IDs:

none

Type:

Family

Sequence Ontology:

SO:0100021

Author:

Bateman A

, Hammonds G

Number in seed:

15

Number in full:

14038

Average length of the domain:

265.1 aa

Average identity of full alignment:

37 %

Average coverage of the sequence by the domain:

34.14 %

HMM information

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	28.9	28.9
Trusted cut-off	28.9	28.9
Noise cut-off	28.8	28.8

Model length:

302

Family (HMM) version:

20

Download:

download the raw HMM for this family

Species distribution

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Archea	Eukaryota
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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...

This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.

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.

In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:

superkingdom
kingdom
phylum
class
order
family
genus
species

Colouring and labels

Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.

As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.

Anomalies in the taxonomy tree

There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.

Missing taxonomic levels

Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.

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.

So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".

Sub-species

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.

Too many species/sequences

For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.

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Tree controls

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The tree shows the occurrence of this domain across different species. More...

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

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.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 Piwi domain has been found. There are 169 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.

Protein	Predicted structure	External Information
A0A044QXY7	View 3D Structure	Click here
A0A044RT47	View 3D Structure	Click here
A0A044S3K3	View 3D Structure	Click here
A0A044SCS0	View 3D Structure	Click here
A0A044U134	View 3D Structure	Click here
A0A044UJK3	View 3D Structure	Click here
A0A044UJT5	View 3D Structure	Click here
A0A044VFS9	View 3D Structure	Click here
A0A077YYT6	View 3D Structure	Click here
A0A077Z0S9	View 3D Structure	Click here
A0A077Z361	View 3D Structure	Click here
A0A077Z610	View 3D Structure	Click here
A0A077ZA53	View 3D Structure	Click here
A0A077ZHP1	View 3D Structure	Click here
A0A077ZKT4	View 3D Structure	Click here
A0A077ZL38	View 3D Structure	Click here
A0A077ZLX5	View 3D Structure	Click here
A0A077ZNM4	View 3D Structure	Click here
A0A077ZNP4	View 3D Structure	Click here
A0A0A2V224	View 3D Structure	Click here
A0A0D2EYD9	View 3D Structure	Click here
A0A0D2G9R6	View 3D Structure	Click here
A0A0D2GUR9	View 3D Structure	Click here
A0A0H5S7K5	View 3D Structure	Click here
A0A0K0DSJ6	View 3D Structure	Click here
A0A0K0E0H6	View 3D Structure	Click here
A0A0K0E1T9	View 3D Structure	Click here
A0A0K0ED42	View 3D Structure	Click here
A0A0K0EEG6	View 3D Structure	Click here
A0A0K0EFP6	View 3D Structure	Click here
A0A0K0EKM9	View 3D Structure	Click here
A0A0K0ENM3	View 3D Structure	Click here
A0A0K0EPK4	View 3D Structure	Click here
A0A0K0ERB3	View 3D Structure	Click here
A0A0K0JDP1	View 3D Structure	Click here
A0A0N4UFD7	View 3D Structure	Click here
A0A0N4UHS2	View 3D Structure	Click here
A0A0N4UKJ1	View 3D Structure	Click here
A0A0P0V142	View 3D Structure	Click here
A0A0P0VVI1	View 3D Structure	Click here

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Family: Piwi (PF02171)

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Summary: Piwi domain

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Argonaute Edit Wikipedia article

References

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Piwi Edit Wikipedia article

References

External links

Piwi domain Provide feedback

Literature references

Internal database links

InterPro entry IPR003165

Gene Ontology

Domain organisation

Pfam Clan

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

Weight segments by...

Change the size of the sunburst

Colour assignments

Selections

Currently selected:

How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

Unmapped species names

Sub-species

Too many species/sequences

Tree controls

Annotation

Download tree

Selected sequences

Species trees

Interactive tree

Structures

AlphaFold Structure Predictions

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