The domain goes by several names including SAD [1], SRA [2] and YDG [3]. It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria [4]. Versions of this domain are known to bind hemi-methylated CpG dinucleotides and also other 5mC containing dinucleotides. The domain binds DNA by flipping out the methylated cytosine base from the DNA double helix [5].The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base [4][5]. Mammalian UHRF1 that contains this domain plays an important role in maintenance of methylation at CpG dinucleotides by recruiting DNMT1 to hemimethylated sites associated with replication forks [2]. The SAD/SRA domain has been combined with other domains involved in the ubiquitin pathway on multiple occasions and such proteins link recognition of DNA methylation to chromatin-protein ubiquitination [4]. The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions [4]. A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains [6]. In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA [4].

1: Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ; Microbiol Mol Biol Rev. 2001;65:44-79. PMID:11238985

2: The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. Sharif J, Muto M, Takebayashi S, Suetake I, Iwamatsu A, Endo TA, Shinga J, Mizutani-Koseki Y, Toyoda T, Okamura K, Tajima S, Mitsuya K, Okano M, Koseki H; Nature. 2007;450:908-912. PMID:17994007

3: The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, Assalkhou R, Schulz I, Reuter G, Aalen RB; Nucleic Acids Res 2001;29:4319-4333. PMID:11691919

4: Natural history of eukaryotic DNA methylation systems. Iyer LM, Abhiman S, Aravind L; Prog Mol Biol Transl Sci. 2011;101:25-104. PMID:21507349

5: Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M; Nature. 2008;455:818-821. PMID:18772891

6: Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Iyer LM, Tahiliani M, Rao A, Aravind L; Cell Cycle. 2009;8:1698-1710. PMID:19411852