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32  structures 169  species 0  interactions 554  sequences 47  architectures

Family: SAD_SRA (PF02182)

Summary: SAD/SRA domain

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This is the Wikipedia entry entitled "YDG SRA protein domain". More...

YDG SRA protein domain Edit Wikipedia article

YDG Set and Ring Associated protein domain
Identifiers
Symbol YDG_SRA
Pfam PF02182
InterPro IPR003105
SMART SRA

In molecular biology, this protein domain has been termed SRA-YDG, which is the abbreviation for SET and Ring finger Associated, YDG motif. Additional characteristics of the domain include conservation of up to 13 evenly spaced glycine residues and a VRV(I/V)RG motif. The protein domain is mainly found in plants and animals and in bacteria.

Function

The function of this protein domain, in animals, is to aid progression through the cell cycle. This domain is associated with the Np95-like ring finger protein and the related gene product Np97, which contains PHD and RING FINGER domains; important 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 needed for the interaction with histones and for chromatin binding in vivo.[1][2]

In plants the SRA-YDG domain is associated with the SET domain, found in a family of histone methyl transferases, which switch genes "off" by adding a methyl group. In bacteria it is found in association with HNH, a non-specific nuclease motif.[2][3]

Structure

This protein domain contains both alpha helices and beta sheets. In particular, the beta sheets are arranged in an antiparallel formation. More specifically, it contains a beta grasp fold.

References

  1. ^ Fujimori A, Matsuda Y, Takemoto Y, Hashimoto Y, Kubo E, Araki R, Fukumura R, Mita K, Tatsumi K, Muto M (December 1998). "Cloning and mapping of Np95 gene which encodes a novel nuclear protein associated with cell proliferation". Mamm. Genome 9 (12): 1032–5. doi:10.1007/s003359900920. PMID 9880673. 
  2. ^ a b Citterio E, Papait R, Nicassio F, Vecchi M, Gomiero P, Mantovani R, Di Fiore PP, Bonapace IM (March 2004). "Np95 is a histone-binding protein endowed with ubiquitin ligase activity". Mol. Cell. Biol. 24 (6): 2526–35. doi:10.1128/MCB.24.6.2526-2535.2004. PMC 355858. PMID 14993289. 
  3. ^ Baumbusch LO, Thorstensen T, Krauss V, Fischer A, Naumann K, Assalkhou R, Schulz I, Reuter G, Aalen RB (November 2001). "The Arabidopsis thaliana genome contains at least 29 active genes encoding SET domain proteins that can be assigned to four evolutionarily conserved classes". Nucleic Acids Res. 29 (21): 4319–33. doi:10.1093/nar/29.21.4319. PMC 60187. PMID 11691919. 

This article incorporates text from the public domain Pfam and InterPro IPR003105

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

SAD/SRA domain Provide feedback

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]. 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].

Literature references

  1. 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

  2. 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

  3. 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

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

  5. 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

  6. 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].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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  Seed
(34)
Full
(554)
Representative proteomes NCBI
(572)
Meta
(41)
RP15
(105)
RP35
(204)
RP55
(288)
RP75
(371)
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  Seed
(34)
Full
(554)
Representative proteomes NCBI
(572)
Meta
(41)
RP15
(105)
RP35
(204)
RP55
(288)
RP75
(371)
Alignment:
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Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(34)
Full
(554)
Representative proteomes NCBI
(572)
Meta
(41)
RP15
(105)
RP35
(204)
RP55
(288)
RP75
(371)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

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Curation and family details

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Curation View help on the curation process

Seed source: Alignment kindly provided by SMART
Previous IDs: G9a; YDG_SRA;
Type: Domain
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.9 21.1
Noise cut-off 20.2 20.3
Model length: 155
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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Structures

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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