PROSITE documentation PDOC50164 [for PROSITE entry PS50164]

GIY-YIG domain profile





Description

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 characterized 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 center and a Glu residue in the C-terminal part [1,2,3,4,5].

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 α/β-sandwich architecture with a central three-stranded antiparallel β-sheet flanked by three-helices (see <PDB:1MK0>). The three-stranded anti-parallel β-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 [2,3,4,5].

Some proteins known to contain a GIY-YIG domain are listed below:

  • Eukaryotic Slx-1 proteins, involved in the maintenance of the rDNA copy number. They have a C-terminal RING finger Zn-binding domain (see <PDOC00449>).
  • Mamalian ankyrin repeat (see <PDOC50088>) and LEM (see <PDOC50954>) 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.

The profile we developed covers the entire GIY-YIG domain.

Last update:

May 2012 / Profile and text revised.

Technical section

PROSITE method (with tools and information) covered by this documentation:

GIY_YIG, PS50164; GIY-YIG domain profile  (MATRIX)


References

1AuthorsKowalski J.C., Belfort M., Stapleton M.A., Holpert M., Dansereau J.T., Pietrokovski S., Baxter S.M., Derbyshire V.
TitleConfiguration of the catalytic GIY-YIG domain of intron endonuclease I-TevI: coincidence of computational and molecular findings.
SourceNucleic Acids Res. 27:2115-2125(1999).
PubMed ID10219084

2AuthorsVan Roey P., Meehan L., Kowalski J.C., Belfort M., Derbyshire V.
TitleCatalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI.
SourceNat. Struct. Biol. 9:806-811(2002).
PubMed ID12379841
DOI10.1038/nsb853

3AuthorsTruglio J.J., Rhau B., Croteau D.L., Wang L., Skorvaga M., Karakas E., DellaVecchia M.J., Wang H., Van Houten B., Kisker C.
TitleStructural insights into the first incision reaction during nucleotide excision repair.
SourceEMBO J. 24:885-894(2005).
PubMed ID15692561
DOI10.1038/sj.emboj.7600568

4AuthorsDunin-Horkawicz S., Feder M., Bujnicki J.M.
TitlePhylogenomic analysis of the GIY-YIG nuclease superfamily.
SourceBMC Genomics 7:98-98(2006).
PubMed ID16646971
DOI10.1186/1471-2164-7-98

5AuthorsIbryashkina E.M., Sasnauskas G., Solonin A.S., Zakharova M.V., Siksnys V.
TitleOligomeric structure diversity within the GIY-YIG nuclease family.
SourceJ. Mol. Biol. 387:10-16(2009).
PubMed ID19361436
DOI10.1016/j.jmb.2009.01.048



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