PROSITE documentation PDOC51015
YDG domain profile


The YDG domain is a 150-170 amino acid long module, which has been named for its characteristic YDG motif. Further characteristics of the domain are the conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif [1]. The YDG domain is found in proteins in combination with different domains, some of which connected with an irreversible enzymatic activity: SET domain (histone methylation) (see <PDOC50280>), RING finger (ubquitination) (see <PDOC00449>), HNH domain (non-specific endonuclease reaction), PHD finger (see <PDOC50016>), AT hook motif, and ubiquitin domain (see <PDOC00271>). As the YDG domain of Np95 has been shown to be indispensable both for interaction with histones and for chromatin binding, it has been proposed that the YDG domain is necessary to direct to the chromatin a number of heterogeneous proteins with associated enzymatic activities [2].

The YDG domain has also been called SIN domain for similarity to ICBP90 and NP95 [3].

Some proteins known to contain a YDG domain are listed below:

  • Mammalian nuclear zinc finger protein Np95 and Np95/ICBP90-like ring finger protein (NIRF), ubiquitin ligases involved in cell cycle regulation and genome stability.
  • Arabidopsis thaliana histone-lysine N-methyltransferases, H3 lysine-9 specific (EC, homologs of suppressor of variegation 3-9.
  • Nicotiana tabacum SET-domain-containing protein (nSET1), involved in the control of plant growth.
  • Deinococcus radiodurans hypothetical protein DR1533.
  • Streptomyces coelicolor hypothetical protein SCO5333.

The profile we developed covers the entire YDG domain.

Last update:

August 2004 / First entry.


Technical section

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

YDG, PS51015; YDG domain profile  (MATRIX)


1AuthorsBaumbusch L.O. Thorstensen T. Krauss V. Fischer A. Naumann K. Assalkhou R. Schulz I. Reuter G. Aalen R.B.
TitleThe Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes.
SourceNucleic Acids Res. 29:4319-4333(2001).
PubMed ID11691919

2AuthorsCitterio E. Papait R. Nicassio F. Vecchi M. Gomiero P. Mantovani R. Di Fiore P.P. Bonapace I.M.
TitleNp95 is a histone-binding protein endowed with ubiquitin ligase activity.
SourceMol. Cell. Biol. 24:2526-2535(2004).
PubMed ID14993289

3TitleShen W.-H. NtSET1, a member of a newly identified subgroup of plant SET-domain-containing proteins, is chromatin-associated and its ectopic overexpression inhibits tobacco plant growth.
SourcePlant J. 28:371-383(2001).
PubMed ID11737775

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