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122  structures 3605  species 0  interactions 18686  sequences 24  architectures

Family: PIN (PF01850)

Summary: PIN domain

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PIN domain Edit Wikipedia article

PIN domain
PDB 1o4w EBI.jpg
Crystal structure of PIN (PilT N-terminus) domain (AF0591) from Archaeoglobus fulgidus at 1.90 Angstrom resolution. 1o4w

In molecular biology the PIN domain is a protein domain that is about 130 amino acids in length. PIN domains function as nuclease enzymes that cleave single stranded RNA in a sequence- or structure-dependent manner.[1][2]

PIN domains contain four nearly invariant acidic residues.[2] 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.[2] These loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress.[3]


  1. ^ Arcus VL, McKenzie JL, Robson J, Cook GM (January 2011). "The PIN-domain ribonucleases and the prokaryotic VapBC toxin-antitoxin array". Protein Engineering, Design & Selection. 24 (1–2): 33–40. doi:10.1093/protein/gzq081. PMID 21036780.
  2. ^ a b c Matelska D, Steczkiewicz K, Ginalski K (July 2017). "Comprehensive classification of the PIN domain-like superfamily". Nucleic Acids Research. 45 (12): 6995–7020. doi:10.1093/nar/gkx494. PMC 5499597. PMID 28575517.
  3. ^ Gerdes K, Christensen SK, Løbner-Olesen A (May 2005). "Prokaryotic toxin-antitoxin stress response loci". Nature Reviews. Microbiology. 3 (5): 371–82. doi:10.1038/nrmicro1147. PMID 15864262.

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PIN domain Provide feedback

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Literature references

  1. 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

  2. Clissold PM, Ponting CP; , Curr Biol 2000;10:888-890.: PIN domains in nonsense-mediated mRNA decay and RNAi. PUBMED:11137022 EPMC:11137022

  3. Gerdes K, Christensen SK, Lobner-Olesen A;, Nat Rev Microbiol. 2005;3:371-382.: Prokaryotic toxin-antitoxin stress response loci. PUBMED:15864262 EPMC:15864262

  4. 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

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 ].

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_N


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Curation and family details

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Curation View help on the curation process

Seed source: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 108
Number in full: 18686
Average length of the domain: 121.80 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 87.69 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.5
Model length: 122
Family (HMM) version: 23
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Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 122 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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