{PDOC50164}
{PS50164; GIY_YIG}
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* GIY-YIG domain profile *
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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 alpha/beta-
sandwich architecture  with  a  central three-stranded antiparallel beta-sheet
flanked by  three-helices  (see  <PDB:1MK0>). 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 [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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: May 2012 / Profile and text revised.

[ 1] Kowalski J.C., Belfort M., Stapleton M.A., Holpert M., Dansereau J.T.,
     Pietrokovski S., Baxter S.M., Derbyshire V.
     "Configuration of the catalytic GIY-YIG domain of intron endonuclease
     I-TevI: coincidence of computational and molecular findings."
     Nucleic Acids Res. 27:2115-2125(1999).
     PubMed=10219084
[ 2] Van Roey P., Meehan L., Kowalski J.C., Belfort M., Derbyshire V.
     "Catalytic domain structure and hypothesis for function of GIY-YIG
     intron endonuclease I-TevI."
     Nat. Struct. Biol. 9:806-811(2002).
     PubMed=12379841; DOI=10.1038/nsb853
[ 3] Truglio J.J., Rhau B., Croteau D.L., Wang L., Skorvaga M., Karakas E.,
     DellaVecchia M.J., Wang H., Van Houten B., Kisker C.
     "Structural insights into the first incision reaction during
     nucleotide excision repair."
     EMBO J. 24:885-894(2005).
     PubMed=15692561; DOI=10.1038/sj.emboj.7600568
[ 4] Dunin-Horkawicz S., Feder M., Bujnicki J.M.
     "Phylogenomic analysis of the GIY-YIG nuclease superfamily."
     BMC Genomics 7:98-98(2006).
     PubMed=16646971; DOI=10.1186/1471-2164-7-98
[ 5] Ibryashkina E.M., Sasnauskas G., Solonin A.S., Zakharova M.V.,
     Siksnys V.
     "Oligomeric structure diversity within the GIY-YIG nuclease family."
     J. Mol. Biol. 387:10-16(2009).
     PubMed=19361436; DOI=10.1016/j.jmb.2009.01.048

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