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169  structures 1613  species 0  interactions 14038  sequences 339  architectures

Family: Piwi (PF02171)

Summary: Piwi domain

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 "Argonaute". More...

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

  1. ^ 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.
  2. ^ 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 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...

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

  1. ^ 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
  2. ^ 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
  3. ^ 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
  4. ^ 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

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

  1. 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

  2. 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

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.

Domain organisation

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

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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
(15)
Full
(14038)
Representative proteomes UniProt
(22300)
RP15
(2628)
RP35
(6003)
RP55
(11131)
RP75
(14647)
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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
(15)
Full
(14038)
Representative proteomes UniProt
(22300)
RP15
(2628)
RP35
(6003)
RP55
(11131)
RP75
(14647)
Alignment:
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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
(15)
Full
(14038)
Representative proteomes UniProt
(22300)
RP15
(2628)
RP35
(6003)
RP55
(11131)
RP75
(14647)
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 View help on the curation process

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 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 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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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