GIY-YIG endonuclease superfamily (IPR035901)
Short name: GIY-YIG_endonuc_sf
- GIY-YIG endonuclease (IPR000305)
- UvrABC system, subunit C (IPR004791)
- Intron endonuclease, group I (IPR006350)
- Excinuclease GIY-YIG catalytic domain-containing uncharacterised conserved protein (IPR014527)
- Bacteriophage T4, DenA, endonuclease II (IPR016413)
- Uncharacterised protein family UPF0213, GIY-YIG endonuclease (IPR022992)
- Structure-specific endonuclease subunit Slx1 (IPR027520)
Nucleases of the GIY-YIG family are involved in many cellular processes, including DNA repair and recombination, transfer of mobile genetic elements, and restriction of incoming foreign DNA. The GIY-YIG superfamily groups together nucleases characterised by the presence of a domain of typically ~100 amino acids, with two short motifs "GIY" and "YIG" in the N-terminal part, followed by an Arg residue in the centre and a Glu residue in the C-terminal part [PMID: 10219084, PMID: 12379841, PMID: 15692561, PMID: 16646971, PMID: 19361436].
The GIY-YIG domain forms a compact structural domain, which serves as a scaffold for the coordination of a divalent metal ion required for catalysis of the phosphodiester bond cleavage. The GIY-YIG domain has an alpha/bera-sandwich architecture with a central three-stranded antiparallel beta-sheet flanked by three-helices. The three-stranded anti-parallel beta-sheet contains the GIY-YIG sequence elements. The most conserved and putative catalytic residues are located on a shallow, concave surface and include a metal coordination site [PMID: 12379841, PMID: 15692561, PMID: 16646971, PMID: 19361436].
The GIY-YIG domain has been implicated in a variety of cellular processes involving DNA cleavage, from self-propagation with or without introns, to restriction of foreign DNA, to DNA repair and maintenance of genome stability [PMID: 16646971].
Some proteins known to contain a GIY-YIG domain include:
- Eukaryotic Slx-1 proteins, involved in the maintenance of the rDNA copy number. They have a C-terminal RING finger Zn-binding domain.
- Mamalian ankyrin repeat and LEM domain- containing protein 1 (ANKLE1).
- Bacterial and archaeal UvrC subunits of (A)BC excinucleases, which remove damaged nucleotides by incising the damaged strand on both sides of the lesion. Paramecium bursaria Chlorella virus 1 (pbvc1).
- Phage T4 endonucleases SegA to E, probably involved in the movement of the endonuclease-encoding DNA.
- Phage T4 intron-associated endonuclease 1 (I-TevI), specific to the thymidylate synthase (td) gene splice junction and involved in intron homing.
This entry represents GIY-YIG nuclease superfamily, and identifies the GIY-YIG domain in diverse and distantly related superfamily members, such as Slx1 [PMID: 16646971].