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Conserved domains on  [gi|985801685|ref|NP_001306876|]
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5' exonuclease Apollo isoform b [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DRMBL super family cl06523
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 90-173 7.35e-13

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


The actual alignment was detected with superfamily member pfam07522:

Pssm-ID: 429512  Cd Length: 108  Bit Score: 64.60  E-value: 7.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985801685   90 LADVFTVEEKAGRIHAVDHMEICHSNMLRW------NQTHPtIAILPTS------------RKIHSSHPDIHV--IPYSD 149
Cdd:pfam07522   3 ILSLLTTDPLSTQIHVVPMPKLSYEALLDYltarkdHFDSV-LAIRPTGwtyrppktevsdRIGPSIRGRITIygVPYSE 81

                          90       100
                  ....*....|....*....|....
gi 985801685  150 HSSYSELRAFVAALKPCQVVPIVS 173
Cdd:pfam07522  82 HSSFDELKEFVQFLRPKKIIPTVN 105
apollo_TRF2_binding cd11662
TRF2-binding region of apollo and similar proteins; Apollo protein, a DNA repair nuclease, is ...
 370-403 2.63e-12

TRF2-binding region of apollo and similar proteins; Apollo protein, a DNA repair nuclease, is recruited to telomeres by TRF2 where it is associated with the principle components of the shelterin complex. Apollo is a member of the metallo-beta-lactamase family that is required for telomere integrity during S phase; its 5' exonuclease activity is regulated by binding to TRF2. Apollo and TRF2 also suppress damage to engineered interstitial telomere repeat tracts at the chromosome ends. TRF2, which binds preferentially to positively supercoiled DNA substrates, together with Apollo, negatively regulates the amount of DNA topoisomerases (TOP1, TOP2-alpha, and TOP2-beta) at telomeres since they also act in the same pathway of telomere protection. The shelterin complex protein identified in mammals is principally comprised of 6 factors that act to protect telomeres from DNA damage repair machinery. 3 components (TRF1, TRF2, POT1) bind DNA and 3 components are recruited by these factors (TIN2, RAP1, TPP1).


:

Pssm-ID: 212560  Cd Length: 34  Bit Score: 60.55  E-value: 2.63e-12
                         10        20        30
                 ....*....|....*....|....*....|....
gi 985801685 370 EFRGLALKYLLTPVNFFQAGYSSRRFDQQVEKYH 403
Cdd:cd11662    1 EPRGLALKYLLTPLNFFQSGFSSRRFDQQVEKYH 34
metallo-hydrolase-like_MBL-fold super family cl23716
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 1-25 3.24e-03

mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain; Members of the MBL-fold metallohydrolase superfamily are mainly hydrolytic enzymes which carry out a variety of biological functions. The class B metal beta-lactamases (MBLs) for which this fold was named perform only a small fraction of the activities included in this superfamily. Activities carried out by superfamily members include class B beta-lactamases which can catalyze the hydrolysis of a wide range of beta-lactam antibiotics, hydroxyacylglutathione hydrolases (also called glyoxalase II) which hydrolyze S-d-lactoylglutathione to d-lactate in the second step of the glycoxlase system, AHL lactonases which catalyze the hydrolysis and opening of the homoserine lactone rings of acyl homoserine lactones (AHLs), persulfide dioxygenase which catalyze the oxidation of glutathione persulfide to glutathione and persulfite in the mitochondria, flavodiiron proteins which catalyze the reduction of oxygen and/or nitric oxide to water or nitrous oxide respectively, cleavage and polyadenylation specificity factors such as the Int9 and Int11 subunits of Integrator, Sdsa1-like and AtsA-like arylsulfatases, 5'-exonucleases human SNM1A and yeast Pso2p, ribonuclease J which has both 5'-3' exoribonucleolytic and endonucleolytic activity and ribonuclease Z which catalyzes the endonucleolytic removal of the 3' extension of the majority of tRNA precursors, cyclic nucleotide phosphodiesterases which decompose cyclic adenosine and guanosine 3', 5'-monophosphate (cAMP and cGMP) respectively, insecticide hydrolases, and proteins required for natural transformation competence. The diversity of biological roles is reflected in variations in the active site metallo-chemistry, for example classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, human persulfide dioxygenase ETHE1 is a mono-iron binding member of the superfamily; Arabidopsis thaliana hydroxyacylglutathione hydrolases incorporates iron, manganese, and zinc in its dinuclear metal binding site, and flavodiiron proteins contains a diiron site.


The actual alignment was detected with superfamily member cd16273:

Pssm-ID: 451500  Cd Length: 160  Bit Score: 37.90  E-value: 3.24e-03
                         10        20
                 ....*....|....*....|....*
gi 985801685   1 MLKEPALTLGKQIHTLYLDNTNCNP 25
Cdd:cd16273  136 MLEHPLLLGKRRIDTVYLDTTYCNP 160
 
Name Accession Description Interval E-value
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 90-173 7.35e-13

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


Pssm-ID: 429512  Cd Length: 108  Bit Score: 64.60  E-value: 7.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985801685   90 LADVFTVEEKAGRIHAVDHMEICHSNMLRW------NQTHPtIAILPTS------------RKIHSSHPDIHV--IPYSD 149
Cdd:pfam07522   3 ILSLLTTDPLSTQIHVVPMPKLSYEALLDYltarkdHFDSV-LAIRPTGwtyrppktevsdRIGPSIRGRITIygVPYSE 81

                          90       100
                  ....*....|....*....|....
gi 985801685  150 HSSYSELRAFVAALKPCQVVPIVS 173
Cdd:pfam07522  82 HSSFDELKEFVQFLRPKKIIPTVN 105
apollo_TRF2_binding cd11662
TRF2-binding region of apollo and similar proteins; Apollo protein, a DNA repair nuclease, is ...
 370-403 2.63e-12

TRF2-binding region of apollo and similar proteins; Apollo protein, a DNA repair nuclease, is recruited to telomeres by TRF2 where it is associated with the principle components of the shelterin complex. Apollo is a member of the metallo-beta-lactamase family that is required for telomere integrity during S phase; its 5' exonuclease activity is regulated by binding to TRF2. Apollo and TRF2 also suppress damage to engineered interstitial telomere repeat tracts at the chromosome ends. TRF2, which binds preferentially to positively supercoiled DNA substrates, together with Apollo, negatively regulates the amount of DNA topoisomerases (TOP1, TOP2-alpha, and TOP2-beta) at telomeres since they also act in the same pathway of telomere protection. The shelterin complex protein identified in mammals is principally comprised of 6 factors that act to protect telomeres from DNA damage repair machinery. 3 components (TRF1, TRF2, POT1) bind DNA and 3 components are recruited by these factors (TIN2, RAP1, TPP1).


Pssm-ID: 212560  Cd Length: 34  Bit Score: 60.55  E-value: 2.63e-12
                         10        20        30
                 ....*....|....*....|....*....|....
gi 985801685 370 EFRGLALKYLLTPVNFFQAGYSSRRFDQQVEKYH 403
Cdd:cd11662    1 EPRGLALKYLLTPLNFFQSGFSSRRFDQQVEKYH 34
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 1-25 3.24e-03

SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) and Saccharomyces cerevisiae Pso2 protein (PSOralen derivative sensitive 2, also known as SNM1, sensitive to nitrogen mustard 1), both proteins are 5'-exonucleases and function in interstrand cross-links (ICL) repair. Also includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein, and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293831  Cd Length: 160  Bit Score: 37.90  E-value: 3.24e-03
                         10        20
                 ....*....|....*....|....*
gi 985801685   1 MLKEPALTLGKQIHTLYLDNTNCNP 25
Cdd:cd16273  136 MLEHPLLLGKRRIDTVYLDTTYCNP 160
 
Name Accession Description Interval E-value
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 90-173 7.35e-13

DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in pfam00753 and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.


Pssm-ID: 429512  Cd Length: 108  Bit Score: 64.60  E-value: 7.35e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985801685   90 LADVFTVEEKAGRIHAVDHMEICHSNMLRW------NQTHPtIAILPTS------------RKIHSSHPDIHV--IPYSD 149
Cdd:pfam07522   3 ILSLLTTDPLSTQIHVVPMPKLSYEALLDYltarkdHFDSV-LAIRPTGwtyrppktevsdRIGPSIRGRITIygVPYSE 81

                          90       100
                  ....*....|....*....|....
gi 985801685  150 HSSYSELRAFVAALKPCQVVPIVS 173
Cdd:pfam07522  82 HSSFDELKEFVQFLRPKKIIPTVN 105
apollo_TRF2_binding cd11662
TRF2-binding region of apollo and similar proteins; Apollo protein, a DNA repair nuclease, is ...
 370-403 2.63e-12

TRF2-binding region of apollo and similar proteins; Apollo protein, a DNA repair nuclease, is recruited to telomeres by TRF2 where it is associated with the principle components of the shelterin complex. Apollo is a member of the metallo-beta-lactamase family that is required for telomere integrity during S phase; its 5' exonuclease activity is regulated by binding to TRF2. Apollo and TRF2 also suppress damage to engineered interstitial telomere repeat tracts at the chromosome ends. TRF2, which binds preferentially to positively supercoiled DNA substrates, together with Apollo, negatively regulates the amount of DNA topoisomerases (TOP1, TOP2-alpha, and TOP2-beta) at telomeres since they also act in the same pathway of telomere protection. The shelterin complex protein identified in mammals is principally comprised of 6 factors that act to protect telomeres from DNA damage repair machinery. 3 components (TRF1, TRF2, POT1) bind DNA and 3 components are recruited by these factors (TIN2, RAP1, TPP1).


Pssm-ID: 212560  Cd Length: 34  Bit Score: 60.55  E-value: 2.63e-12
                         10        20        30
                 ....*....|....*....|....*....|....
gi 985801685 370 EFRGLALKYLLTPVNFFQAGYSSRRFDQQVEKYH 403
Cdd:cd11662    1 EPRGLALKYLLTPLNFFQSGFSSRRFDQQVEKYH 34
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 1-25 3.24e-03

SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) and Saccharomyces cerevisiae Pso2 protein (PSOralen derivative sensitive 2, also known as SNM1, sensitive to nitrogen mustard 1), both proteins are 5'-exonucleases and function in interstrand cross-links (ICL) repair. Also includes the nuclease artemis (also known as SNM1C, SNM1 homolog C, SNM1-like protein, and DNA cross-link repair 1C protein) which plays a role in V(D)J recombination/DNA repair. Purified artemis protein possesses single-strand-specific 5' to 3' exonuclease activity. Upon complex formation with, and phosphorylation by, DNA-dependent protein kinase, artemis gains endonucleolytic activity on hairpins and 5' and 3' overhangs. Members of this subgroup belong to the MBL-fold metallo-hydrolase superfamily which is comprised mainly of hydrolytic enzymes which carry out a variety of biological functions.


Pssm-ID: 293831  Cd Length: 160  Bit Score: 37.90  E-value: 3.24e-03
                         10        20
                 ....*....|....*....|....*
gi 985801685   1 MLKEPALTLGKQIHTLYLDNTNCNP 25
Cdd:cd16273  136 MLEHPLLLGKRRIDTVYLDTTYCNP 160
 
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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