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Conserved domains on  [gi|15238020|ref|NP_199526|]
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YDG/SRA domain-containing protein [Arabidopsis thaliana]

Protein Classification

YDG/SRA domain-containing protein( domain architecture ID 10490222)

YDG/SRA domain-containing protein adopts a beta barrel, modified PUA-like fold that binds hemi-methylated CpG dinucleotides and other 5mC containing dinucleotides

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
 174-322 9.35e-59

SAD/SRA domain; 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.


:

Pssm-ID: 460476  Cd Length: 146  Bit Score: 185.83  E-value: 9.35e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020   174 RIGSVPGINIGDVFQYKTELRVVGLHSKPMCGIDYIKlgdDRITTSIVASEGYGyNDTYNSGVMVYTGEGGNVINKQKKT 253
Cdd:pfam02182   1 RFGHVPGVEVGDIFSSRAELCVVGLHRPTQAGIDGMK---SEGAYSIVLSGGYE-DDEDNGDVLIYTGSGGRDNTKKKQS 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020   254 EDQKLVKGNLALATSMRQKSQVRVIRGEER-LDRKGKRYVYDGLYMVEEYWVERDVRGKSVYKFKLCRIP 322
Cdd:pfam02182  77 ADQKLERGNLALANSCETGNPVRVIRGSKRdSYPPKKGYRYDGLYKVEKYWEEKGKSGFLVFKFKLRRLP 146
 
Name Accession Description Interval E-value
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
 174-322 9.35e-59

SAD/SRA domain; 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.


Pssm-ID: 460476  Cd Length: 146  Bit Score: 185.83  E-value: 9.35e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020   174 RIGSVPGINIGDVFQYKTELRVVGLHSKPMCGIDYIKlgdDRITTSIVASEGYGyNDTYNSGVMVYTGEGGNVINKQKKT 253
Cdd:pfam02182   1 RFGHVPGVEVGDIFSSRAELCVVGLHRPTQAGIDGMK---SEGAYSIVLSGGYE-DDEDNGDVLIYTGSGGRDNTKKKQS 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020   254 EDQKLVKGNLALATSMRQKSQVRVIRGEER-LDRKGKRYVYDGLYMVEEYWVERDVRGKSVYKFKLCRIP 322
Cdd:pfam02182  77 ADQKLERGNLALANSCETGNPVRVIRGSKRdSYPPKKGYRYDGLYKVEKYWEEKGKSGFLVFKFKLRRLP 146
SRA smart00466
SET and RING finger associated domain; Domain of unknown function in SET domain containing ...
 172-324 2.13e-54

SET and RING finger associated domain; Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533.


Pssm-ID: 197742  Cd Length: 155  Bit Score: 174.86  E-value: 2.13e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020    172 EKRIGSVPGINIGDVFQYKTELRVVGLHSKPMCGIDYIKLGD-DRITTSIVASEGYGyNDTYNSGVMVYTGEGGNViNKQ 250
Cdd:smart00466   2 KRIFGPVPGVEVGDIFFYRVELCLVGLHRPTQAGIDGLESDEgEPGATSVVSSGGYE-DDTDDGDVLIYTGQGGRD-MTH 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238020    251 KKTEDQKLVKGNLALATSMRQKSQVRVIRGEERLDRK--GKRYVYDGLYMVEEYWVERDVRGKSVYKFKLCRIPGQ 324
Cdd:smart00466  80 GQPEDQKLERGNLALEASCRKGIPVRVVRGMKGYSKYapGKGYIYDGLYRIVDYWREVGKSGFLVFKFKLVRIPGQ 155
 
Name Accession Description Interval E-value
SAD_SRA pfam02182
SAD/SRA domain; The domain goes by several names including SAD, SRA and YDG. It adopts a beta ...
 174-322 9.35e-59

SAD/SRA domain; 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.


Pssm-ID: 460476  Cd Length: 146  Bit Score: 185.83  E-value: 9.35e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020   174 RIGSVPGINIGDVFQYKTELRVVGLHSKPMCGIDYIKlgdDRITTSIVASEGYGyNDTYNSGVMVYTGEGGNVINKQKKT 253
Cdd:pfam02182   1 RFGHVPGVEVGDIFSSRAELCVVGLHRPTQAGIDGMK---SEGAYSIVLSGGYE-DDEDNGDVLIYTGSGGRDNTKKKQS 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020   254 EDQKLVKGNLALATSMRQKSQVRVIRGEER-LDRKGKRYVYDGLYMVEEYWVERDVRGKSVYKFKLCRIP 322
Cdd:pfam02182  77 ADQKLERGNLALANSCETGNPVRVIRGSKRdSYPPKKGYRYDGLYKVEKYWEEKGKSGFLVFKFKLRRLP 146
SRA smart00466
SET and RING finger associated domain; Domain of unknown function in SET domain containing ...
 172-324 2.13e-54

SET and RING finger associated domain; Domain of unknown function in SET domain containing proteins and in Deinococcus radiodurans DRA1533.


Pssm-ID: 197742  Cd Length: 155  Bit Score: 174.86  E-value: 2.13e-54
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15238020    172 EKRIGSVPGINIGDVFQYKTELRVVGLHSKPMCGIDYIKLGD-DRITTSIVASEGYGyNDTYNSGVMVYTGEGGNViNKQ 250
Cdd:smart00466   2 KRIFGPVPGVEVGDIFFYRVELCLVGLHRPTQAGIDGLESDEgEPGATSVVSSGGYE-DDTDDGDVLIYTGQGGRD-MTH 79

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15238020    251 KKTEDQKLVKGNLALATSMRQKSQVRVIRGEERLDRK--GKRYVYDGLYMVEEYWVERDVRGKSVYKFKLCRIPGQ 324
Cdd:smart00466  80 GQPEDQKLERGNLALEASCRKGIPVRVVRGMKGYSKYapGKGYIYDGLYRIVDYWREVGKSGFLVFKFKLVRIPGQ 155
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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