In molecular biology the PIN domain is a protein domain

Protein domain

A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...

 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

Nuclease

A nuclease is an enzyme capable of cleaving the phosphodiester bonds between the nucleotide subunits of nucleic acids. Older publications may use terms such as "polynucleotidase" or "nucleodepolymerase"....

 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

Active site

In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...

. In eukaryotes PIN domains are found in proteins involved in nonsense mediated mRNA decay

Nonsense mediated decay

Nonsense-mediated decay is a cellular mechanism of mRNA surveillance that functions to detect nonsense mutations and prevent the expression of truncated or erroneous proteins. Following transcription, precursor mRNA undergoes an assemblage of ribonucleoprotein components followed by regulatory...

, in proteins such as SMG5

SMG5

Protein SMG5 is a protein that in humans is encoded by the SMG5 gene. This protein contains a PIN domain that appears to have mutated the residues in the active site.-Further reading:...

 and SMG6

SMG6

Telomerase-binding protein EST1A is an enzyme that in humans is encoded by the SMG6 gene. The C-terminus of the EST1A protein contains a PIN domain. This structure for this domain has been determined by X-ray crystallography.-Further reading:...

, and in processing of 18S ribosomal RNA

Ribosomal RNA

Ribosomal ribonucleic acid is the RNA component of the ribosome, the enzyme that is the site of protein synthesis in all living cells. Ribosomal RNA provides a mechanism for decoding mRNA into amino acids and interacts with tRNAs during translation by providing peptidyl transferase activity...

. The majority of PIN-domain proteins found in prokaryotes are the toxic components of toxin-antitoxin operon

Toxin-antitoxin system

A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a protein 'poison' and a corresponding 'antidote'. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid...

, and toxin-antitoxin gene cassettes, These loci provide a control mechanism that helps free-living prokaryotes cope with nutritional stress.