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125  structures 3664  species 0  interactions 19626  sequences 24  architectures

Family: PIN (PF01850)

Summary: PIN domain

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This is the Wikipedia entry entitled "PIN domain". More...

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​
Identifiers
SymbolPIN
PfamPF01850
InterProIPR002716
SMARTCBS
SCOP23dbo / SCOPe / SUPFAM

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

  1. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  2. ^ 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. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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PIN domain Provide feedback

No Pfam abstract.

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

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...

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
(108)
Full
(19626)
Representative proteomes UniProt
(108783)
RP15
(3184)
RP35
(10408)
RP55
(20912)
RP75
(35709)
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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
(108)
Full
(19626)
Representative proteomes UniProt
(108783)
RP15
(3184)
RP35
(10408)
RP55
(20912)
RP75
(35709)
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
(108)
Full
(19626)
Representative proteomes UniProt
(108783)
RP15
(3184)
RP35
(10408)
RP55
(20912)
RP75
(35709)
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: [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 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 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.5
Model length: 122
Family (HMM) version: 24
Download: download the raw HMM for this family

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

Selections

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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.

Protein Predicted structure External Information
A0A077ZG98 View 3D Structure Click here
A0A0H3GPK8 View 3D Structure Click here
A0A0H3GYM2 View 3D Structure Click here
A0QRY6 View 3D Structure Click here
K0EHS7 View 3D Structure Click here
K0EM23 View 3D Structure Click here
K0EMT8 View 3D Structure Click here
K0ETD5 View 3D Structure Click here
K0EWE8 View 3D Structure Click here
K0EWP8 View 3D Structure Click here
K0F2Z0 View 3D Structure Click here
K0F4A5 View 3D Structure Click here
K0F5Z9 View 3D Structure Click here
K0F790 View 3D Structure Click here
K0F8S3 View 3D Structure Click here
K0F8W5 View 3D Structure Click here
K0F9B9 View 3D Structure Click here
L0T5V6 View 3D Structure Click here
O06662 View 3D Structure Click here
O07783 View 3D Structure Click here
O28590 View 3D Structure Click here
O50411 View 3D Structure Click here
O53219 View 3D Structure Click here
O53501 View 3D Structure Click here
O53779 View 3D Structure Click here
O66399 View 3D Structure Click here
O67739 View 3D Structure Click here
P55511 View 3D Structure Click here
P71363 View 3D Structure Click here
P71623 View 3D Structure Click here
P95004 View 3D Structure Click here
P95007 View 3D Structure Click here
P96917 View 3D Structure Click here
P9WF47 View 3D Structure Click here
P9WF49 View 3D Structure Click here
P9WF51 View 3D Structure Click here
P9WF53 View 3D Structure Click here
P9WF55 View 3D Structure Click here
P9WF57 View 3D Structure Click here
P9WF59 View 3D Structure Click here