Summary: PIN domain
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PIN domain Edit Wikipedia article
PIN domain | |||||||||||
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![]() Crystal structure of PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 Angstrom resolution. 1o4w​ | |||||||||||
Identifiers | |||||||||||
Symbol | PIN | ||||||||||
Pfam | PF01850 | ||||||||||
InterPro | IPR002716 | ||||||||||
SMART | CBS | ||||||||||
SCOP2 | 3dbo / SCOPe / SUPFAM | ||||||||||
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In molecular biology the PIN domain is a protein domain that is about 130 amino acids in length. The PIN domain was named after its identification in the N-nerminus of the PilT protein (PilT N terminus). PIN domains function as nuclease enzymes that cleave single stranded RNA in a sequence dependent manner.[1]
PIN domains contain three nearly invariant acidic residues. Crystal structures show these residues clustered together in the putative active site. In eukaryotes PIN domains are found in proteins involved in nonsense mediated mRNA decay and processing of 18S ribosomal RNA. The majority of PIN-domain proteins found in prokaryotes are the toxic components of toxin-antitoxin operon, and toxin-antitoxin gene cassettes, These loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress.[2]
References
- ^ Arcus VL, McKenzie JL, Robson J, Cook GM (2011). "The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array". Protein Eng. Des. Sel. 24 (1–2): 33–40. doi:10.1093/protein/gzq081. PMID 21036780.
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ignored (help)CS1 maint: multiple names: authors list (link) - ^ Gerdes K, Christensen SK, Løbner-Olesen A (2005). "Prokaryotic toxin-antitoxin stress response loci". Nat. Rev. Microbiol. 3 (5): 371–82. doi:10.1038/nrmicro1147. PMID 15864262.
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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.
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Literature references
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Makarova KS, Aravind L, Galperin MY, Grishin NV, Tatusov RL, Wolf YI, Koonin EV; , Genome Res 1999;9:608-628.: Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. PUBMED:10413400 EPMC:10413400
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Clissold PM, Ponting CP; , Curr Biol 2000;10:888-890.: PIN domains in nonsense-mediated mRNA decay and RNAi. PUBMED:11137022 EPMC:11137022
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Gerdes K, Christensen SK, Lobner-Olesen A;, Nat Rev Microbiol. 2005;3:371-382.: Prokaryotic toxin-antitoxin stress response loci. PUBMED:15864262 EPMC:15864262
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Arcus VL, Rainey PB, Turner SJ;, Trends Microbiol. 2005;13:360-365.: The PIN-domain toxin-antitoxin array in mycobacteria. PUBMED:15993073 EPMC:15993073
Internal database links
SCOOP: | DUF4411 DUF5615 PIN_12 PIN_2 PIN_3 PIN_4 PIN_8 PIN_9 |
Similarity to PfamA using HHSearch: | PIN_2 PIN_3 DUF4411 |
External database links
SCOP: | 1o4w |
This tab holds annotation information from the InterPro database.
InterPro entry IPR002716
PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation [ PUBMED:21036780 ]. PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay [ PUBMED:17053788 ] and in processing of 18S ribosomal RNA [ PUBMED:19706509 ]. In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin [ PUBMED:21036780 ].
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 PIN (CL0280), which has the following description:
This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.
The clan contains the following 27 members:
5_3_exonuc_N DUF1308 DUF188 DUF4411 DUF5615 DUF5616 Fcf1 Mut7-C NYN NYN_YacP PIN PIN7 PIN_10 PIN_11 PIN_12 PIN_2 PIN_3 PIN_4 PIN_5 PIN_6 PIN_8 PIN_9 PRORP RNase_Zc3h12a RNase_Zc3h12a_2 XPG_N XRN_NAlignments
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 (108) |
Full (19626) |
Representative proteomes | UniProt (108783) |
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RP15 (3184) |
RP35 (10408) |
RP55 (20912) |
RP75 (35709) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (108) |
Full (19626) |
Representative proteomes | UniProt (108783) |
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---|---|---|---|---|---|---|---|
RP15 (3184) |
RP35 (10408) |
RP55 (20912) |
RP75 (35709) |
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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: | [1] |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 108 |
Number in full: | 19626 |
Average length of the domain: | 121.8 aa |
Average identity of full alignment: | 16 % |
Average coverage of the sequence by the domain: | 87.76 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 122 | ||||||||||||
Family (HMM) version: | 24 | ||||||||||||
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 PIN domain has been found. There are 125 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.