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Conserved domains on  [gi|76496495|ref|NP_071932|]
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protein artemis isoform b [Homo sapiens]

Protein Classification

DNA cross-link repair protein( domain architecture ID 11039898)

DNA cross-link repair protein similar to Arabidopsis thaliana SNM1, which is involved in the repair of DNA lesions formed by oxidative stress

Gene Ontology:  GO:0006974|GO:0005634
PubMed:  12177301|20528238

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
124-230 8.88e-30

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: 113.14  E-value: 8.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76496495   124 PEILHHLTTD-RNTQIHACRHPKAEeyfqWSKLPCGITSRNRIPLHIISIKPSTmwFGERSRKTNVIVRTGES------S 196
Cdd:pfam07522   1 PEILSLLTTDpLSTQIHVVPMPKLS----YEALLDYLTARKDHFDSVLAIRPTG--WTYRPPKTEVSDRIGPSirgritI 74
                          90       100       110
                  ....*....|....*....|....*....|....
gi 76496495   197 YRACFSFHSSYSEIKDFLSYLCPVNAYPNVIPVG 230
Cdd:pfam07522  75 YGVPYSEHSSFDELKEFVQFLRPKKIIPTVNVGG 108
metallo-hydrolase-like_MBL-fold super family cl23716
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
7-56 1.44e-29

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 cd16297:

Pssm-ID: 451500  Cd Length: 171  Bit Score: 114.53  E-value: 1.44e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 76496495   7 FLFQGNNGTVLYTGDFRLAQGEAARMELLHSGGRVKDIQSVYLDTTFCDP 56
Cdd:cd16297 122 FLFQGNNGTVLYTGDFRLAVGEAARMELLHSGDRVKDIQSVYLDTTFCDP 171
 
Name Accession Description Interval E-value
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
124-230 8.88e-30

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: 113.14  E-value: 8.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76496495   124 PEILHHLTTD-RNTQIHACRHPKAEeyfqWSKLPCGITSRNRIPLHIISIKPSTmwFGERSRKTNVIVRTGES------S 196
Cdd:pfam07522   1 PEILSLLTTDpLSTQIHVVPMPKLS----YEALLDYLTARKDHFDSVLAIRPTG--WTYRPPKTEVSDRIGPSirgritI 74
                          90       100       110
                  ....*....|....*....|....*....|....
gi 76496495   197 YRACFSFHSSYSEIKDFLSYLCPVNAYPNVIPVG 230
Cdd:pfam07522  75 YGVPYSEHSSFDELKEFVQFLRPKKIIPTVNVGG 108
artemis-SNM1C-like_MBL-fold cd16297
artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease ...
7-56 1.44e-29

artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; 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. Inactivation of Artemis causes severe combined immunodeficiency (SCID). 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: 293855  Cd Length: 171  Bit Score: 114.53  E-value: 1.44e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 76496495   7 FLFQGNNGTVLYTGDFRLAQGEAARMELLHSGGRVKDIQSVYLDTTFCDP 56
Cdd:cd16297 122 FLFQGNNGTVLYTGDFRLAVGEAARMELLHSGDRVKDIQSVYLDTTFCDP 171
 
Name Accession Description Interval E-value
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
124-230 8.88e-30

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: 113.14  E-value: 8.88e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 76496495   124 PEILHHLTTD-RNTQIHACRHPKAEeyfqWSKLPCGITSRNRIPLHIISIKPSTmwFGERSRKTNVIVRTGES------S 196
Cdd:pfam07522   1 PEILSLLTTDpLSTQIHVVPMPKLS----YEALLDYLTARKDHFDSVLAIRPTG--WTYRPPKTEVSDRIGPSirgritI 74
                          90       100       110
                  ....*....|....*....|....*....|....
gi 76496495   197 YRACFSFHSSYSEIKDFLSYLCPVNAYPNVIPVG 230
Cdd:pfam07522  75 YGVPYSEHSSFDELKEFVQFLRPKKIIPTVNVGG 108
artemis-SNM1C-like_MBL-fold cd16297
artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease ...
7-56 1.44e-29

artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; 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. Inactivation of Artemis causes severe combined immunodeficiency (SCID). 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: 293855  Cd Length: 171  Bit Score: 114.53  E-value: 1.44e-29
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 76496495   7 FLFQGNNGTVLYTGDFRLAQGEAARMELLHSGGRVKDIQSVYLDTTFCDP 56
Cdd:cd16297 122 FLFQGNNGTVLYTGDFRLAVGEAARMELLHSGDRVKDIQSVYLDTTFCDP 171
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
7-56 6.56e-10

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: 57.94  E-value: 6.56e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 76496495   7 FLFQGNNG-TVLYTGDFRLAQGEAARMELLHSggrvKDIQSVYLDTTFCDP 56
Cdd:cd16273 114 FLFELPDGrRILHTGDFRANPEMLEHPLLLGK----RRIDTVYLDTTYCNP 160
SNM1A-like_MBL-fold cd16298
5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes ...
8-56 9.00e-03

5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes human SNM1A (SNM1 homolog A, also known as DNA cross-link repair 1A protein) which is a 5'-exonuclease and functions in interstrand cross-links (ICL) repair. 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: 293856 [Multi-domain]  Cd Length: 157  Bit Score: 37.11  E-value: 9.00e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 76496495   8 LFQGNNGT-VLYTGDFRlAQGEAARMELLHSggrvKDIQSVYLDTTFCDP 56
Cdd:cd16298 113 LFRLPSGTlVLHTGDFR-ADPSMERYPELIG----QKIHTLYLDTTYCSP 157
 
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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