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Conserved domains on  [gi|1063721646|ref|NP_001319897|]
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DDE family endonuclease [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 245-314 3.17e-19

Protein of unknown function (DUF2439); This domain can be found in proteins that have been implicated in telomere maintenance in Saccharomyces cerevisiae and in meiotic chromosome segregation in Schizosaccharomyces pombe. It can also be found in Mte1 (Mph1-associated telomere maintenance protein 1), human zinc finger protein ZGRF1 (C4ORF21) and fission yeast Dbl2. Mte1 is a D-loop-binding protein that interacts and stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres. Mte1 is indicated to play a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. The fission yeast, Dbl2 is needed for cellular resistance to the topoisomerase I poison camptothecin, forms DNA damage-induced foci, and is needed for the optimal recruitment of Fml1 to DNA damage, while the human ZGRF1 protein has been linked to DNA cross-link repair and mutations of it have been found in a variety of human tumors. ZGRF1 is a 5'-to-3'helicase that interacts with RAD51 and stimulates homologous recombination and, thus, promotes the repair of replication-blocking DNA lesions. Having said that, there is no evidence to suggest that this domain is implicated in DNA damage resistance or for nuclear focus formation.


:

Pssm-ID: 463065  Cd Length: 74  Bit Score: 81.78  E-value: 3.17e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063721646 245 QRWIAMYTKHLKQKRKVYHDGFLDLHIARKKVMLYDEDDNLLESRTLKACEVVNTGETLTFQAYLVDICD 314
Cdd:pfam10382   2 HEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVMLYDEDGNLIGSDFWTSSEDLEEGEELELDRYLVQIEE 71
DDE_Tnp_4 super family cl48181
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 72-160 8.18e-05

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.


The actual alignment was detected with superfamily member pfam13359:

Pssm-ID: 463855 [Multi-domain]  Cd Length: 158  Bit Score: 43.03  E-value: 8.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063721646  72 HDTKVLKYCARNESFSPHPSNRKYYLVNSVYPTTTGYLGPHRrilyhlgqfGRGGPPVTVQEL-FNRKHLDLRSVIDRTF 150
Cdd:pfam13359  54 SDKSILENSGLLKALNLAFGPGDYILADKGFPISDWLLVPYK---------KPGGAQLSPEEVeFNRRIASARIHVERVI 124

                          90
                  ....*....|
gi 1063721646 151 GVWKAKWRIL 160
Cdd:pfam13359 125 GRLKGRFRIL 134
 
Name Accession Description Interval E-value
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 245-314 3.17e-19

Protein of unknown function (DUF2439); This domain can be found in proteins that have been implicated in telomere maintenance in Saccharomyces cerevisiae and in meiotic chromosome segregation in Schizosaccharomyces pombe. It can also be found in Mte1 (Mph1-associated telomere maintenance protein 1), human zinc finger protein ZGRF1 (C4ORF21) and fission yeast Dbl2. Mte1 is a D-loop-binding protein that interacts and stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres. Mte1 is indicated to play a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. The fission yeast, Dbl2 is needed for cellular resistance to the topoisomerase I poison camptothecin, forms DNA damage-induced foci, and is needed for the optimal recruitment of Fml1 to DNA damage, while the human ZGRF1 protein has been linked to DNA cross-link repair and mutations of it have been found in a variety of human tumors. ZGRF1 is a 5'-to-3'helicase that interacts with RAD51 and stimulates homologous recombination and, thus, promotes the repair of replication-blocking DNA lesions. Having said that, there is no evidence to suggest that this domain is implicated in DNA damage resistance or for nuclear focus formation.


Pssm-ID: 463065  Cd Length: 74  Bit Score: 81.78  E-value: 3.17e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063721646 245 QRWIAMYTKHLKQKRKVYHDGFLDLHIARKKVMLYDEDDNLLESRTLKACEVVNTGETLTFQAYLVDICD 314
Cdd:pfam10382   2 HEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVMLYDEDGNLIGSDFWTSSEDLEEGEELELDRYLVQIEE 71
DDE_Tnp_4 pfam13359
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 72-160 8.18e-05

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.


Pssm-ID: 463855 [Multi-domain]  Cd Length: 158  Bit Score: 43.03  E-value: 8.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063721646  72 HDTKVLKYCARNESFSPHPSNRKYYLVNSVYPTTTGYLGPHRrilyhlgqfGRGGPPVTVQEL-FNRKHLDLRSVIDRTF 150
Cdd:pfam13359  54 SDKSILENSGLLKALNLAFGPGDYILADKGFPISDWLLVPYK---------KPGGAQLSPEEVeFNRRIASARIHVERVI 124

                          90
                  ....*....|
gi 1063721646 151 GVWKAKWRIL 160
Cdd:pfam13359 125 GRLKGRFRIL 134
 
Name Accession Description Interval E-value
DUF2439 pfam10382
Protein of unknown function (DUF2439); This domain can be found in proteins that have been ...
 245-314 3.17e-19

Protein of unknown function (DUF2439); This domain can be found in proteins that have been implicated in telomere maintenance in Saccharomyces cerevisiae and in meiotic chromosome segregation in Schizosaccharomyces pombe. It can also be found in Mte1 (Mph1-associated telomere maintenance protein 1), human zinc finger protein ZGRF1 (C4ORF21) and fission yeast Dbl2. Mte1 is a D-loop-binding protein that interacts and stimulates the helicase and fork regression activities of Mph1 while inhibiting the ability of Mph1 to dissociate recombination intermediates. Mph1 and Mte1 interdependently colocalize at DNA damage-induced foci and dysfunctional telomeres. Mte1 is indicated to play a role in regulation of crossover recombination, response to replication stress, and telomere maintenance. The fission yeast, Dbl2 is needed for cellular resistance to the topoisomerase I poison camptothecin, forms DNA damage-induced foci, and is needed for the optimal recruitment of Fml1 to DNA damage, while the human ZGRF1 protein has been linked to DNA cross-link repair and mutations of it have been found in a variety of human tumors. ZGRF1 is a 5'-to-3'helicase that interacts with RAD51 and stimulates homologous recombination and, thus, promotes the repair of replication-blocking DNA lesions. Having said that, there is no evidence to suggest that this domain is implicated in DNA damage resistance or for nuclear focus formation.


Pssm-ID: 463065  Cd Length: 74  Bit Score: 81.78  E-value: 3.17e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063721646 245 QRWIAMYTKHLKQKRKVYHDGFLDLHIARKKVMLYDEDDNLLESRTLKACEVVNTGETLTFQAYLVDICD 314
Cdd:pfam10382   2 HEYRCLYTHDVRKKHKRWHDGKLKYHTFNKRVMLYDEDGNLIGSDFWTSSEDLEEGEELELDRYLVQIEE 71
DDE_Tnp_4 pfam13359
DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are ...
 72-160 8.18e-05

DDE superfamily endonuclease; This family of proteins are related to pfam00665 and are probably endonucleases of the DDE superfamily. Transposase proteins are necessary for efficient DNA transposition. This domain is a member of the DDE superfamily, which contain three carboxylate residues that are believed to be responsible for coordinating metal ions needed for catalysis. The catalytic activity of this enzyme involves DNA cleavage at a specific site followed by a strand transfer reaction.


Pssm-ID: 463855 [Multi-domain]  Cd Length: 158  Bit Score: 43.03  E-value: 8.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063721646  72 HDTKVLKYCARNESFSPHPSNRKYYLVNSVYPTTTGYLGPHRrilyhlgqfGRGGPPVTVQEL-FNRKHLDLRSVIDRTF 150
Cdd:pfam13359  54 SDKSILENSGLLKALNLAFGPGDYILADKGFPISDWLLVPYK---------KPGGAQLSPEEVeFNRRIASARIHVERVI 124

                          90
                  ....*....|
gi 1063721646 151 GVWKAKWRIL 160
Cdd:pfam13359 125 GRLKGRFRIL 134
 
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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