Summary: SAD/SRA domain
SAD/SRA domain Provide feedback
The domain goes by several names including SAD  SRA  and YDG . It adopts a beta barrel, modified PUA-like, fold that is widely present in eukaryotic chromatin proteins and in bacteria . 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 .The conserved tyrosine and aspartate residues and a glycine rich patch are critical for recognition of the flipped out base . 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 . 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 . The domain is also found in species that lack DNA methylation, such as certain apicomplexans, suggestive of other DNA-binding modes or functions . A highly derived and distinct version of the domain is also found in fungi where it is fused to AlkB-type 2OGFeDO domains . In bacteria, the domain is usually fused or associated with restriction endonucleases, many of which target methylated or hemi-methylated DNA .
Makarova KS, Aravind L, Wolf YI, Tatusov RL, Minton KW, Koonin EV, Daly MJ;, Microbiol Mol Biol Rev. 2001;65:44-79.: Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. PUBMED:11238985 EPMC:11238985
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.: The SRA protein Np95 mediates epigenetic inheritance by recruiting Dnmt1 to methylated DNA. PUBMED:17994007 EPMC:17994007
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.: The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes. PUBMED:11691919 EPMC:11691919
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M;, Nature. 2008;455:818-821.: Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. PUBMED:18772891 EPMC:18772891
Iyer LM, Tahiliani M, Rao A, Aravind L;, Cell Cycle. 2009;8:1698-1710.: Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. PUBMED:19411852 EPMC:19411852
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003105
This domain has been termed SRA-YDG, for SET and Ring finger Associated, and because of the conserved YDG motif within the domain. Further characteristics of the domain are the conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The domain is mainly found in plants and animals and in bacteria. In animals, this domain is associated with the Np95-like ring finger protein and the related gene product Np97, which contains PHD and RING FINGER domains and which is an important determinant in cell cycle progression. Np95 is a chromatin-associated ubiquitin ligase, binding to histones is direct and shows a remarkable preference for histone H3 and its N-terminal tail. The SRA-YDG domain contained in Np95 is indispensable both for the interaction with histones and for chromatin binding in vivo [PUBMED:9880673, PUBMED:14993289]. In plants the SRA-YDG domain is associated with the SET domain, found in a family of histone methyl transferases, and in bacteria it is found in association with HNH, a non-specific nuclease motif [PUBMED:14993289, PUBMED:11691919].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||histone binding (GO:0042393)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
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We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Alignment kindly provided by SMART|
|Previous IDs:||G9a; YDG_SRA;|
|Author:||Iyer LM, Aravind L, SMART|
|Number in seed:||34|
|Number in full:||554|
|Average length of the domain:||149.00 aa|
|Average identity of full alignment:||37 %|
|Average coverage of the sequence by the domain:||23.53 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the SAD_SRA domain has been found. There are 32 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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