Summary: PIN domain
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PIN domain Edit Wikipedia article
Crystal structure of PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 Angstrom resolution.
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-terminus of the PilT protein (PilT N terminus). PIN domains function as nuclease enzymes that cleave single stranded RNA in a sequence dependent manner.
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, in proteins such as SMG5 and SMG6, and in processing of 18S ribosomal RNA. The majority of PIN-domain proteins found in prokaryotes are the toxic components of toxin-antitoxin operons. These loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress.
- Arcus VL, McKenzie JL, Robson J, Cook GM (January 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.
- Gerdes K, Christensen SK, Løbner-Olesen A (May 2005). "Prokaryotic toxin-antitoxin stress response loci". Nat. Rev. Microbiol. 3 (5): 371–82. doi:10.1038/nrmicro1147. PMID 15864262.
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Members of this family of bacterial domains are predicted to be RNases (from similarities to 5'-exonucleases).
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External database links
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].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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This superfamily contains a variety of nuclease enzymes, including PIN domains and the FLAP exonucleases.
The clan contains the following 17 members:5_3_exonuc_N DUF188 DUF4411 Fcf1 Mut7-C NYN NYN_YacP PIN PIN_2 PIN_3 PIN_4 PRORP RNase_Zc3h12a RNase_Zc3h12a_2 UPF0278 XPG_N XRN_N
We make a range of alignments for each Pfam-A family:
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Number in seed:||107|
|Number in full:||6649|
|Average length of the domain:||139.50 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||26.48 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There is 1 interaction for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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_4 domain has been found. There are 10 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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