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Conserved domains on  [gi|568912361|ref|XP_006497518|]
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protein artemis isoform X5 [Mus musculus]

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
metallo-hydrolase-like_MBL-fold super family cl23716
mainly hydrolytic enzymes and related proteins which carry out various biological functions; ...
 3-91 4.24e-57

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: 190.03  E-value: 4.24e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361   3 ITIEIETPTQISLVDEASGEKEEVVVTLLPAGHCPGSVMFLFQGSNGTVLYTGDFRLAKGEASRMELLHSGGRVKDIQSV 82
Cdd:cd16297   83 VSLEIDTPTQISLVDEATGEKEDVVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAVGEAARMELLHSGDRVKDIQSV 162


                 ....*....
gi 568912361  83 YLDTTFCDP 91
Cdd:cd16297  163 YLDTTFCDP 171
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 159-265 9.21e-29

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: 110.44  E-value: 9.21e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361  159 PDILHHLTTD-RNTQIHACRHPKAEecfqWNKLPCGITSQNKTALHTISIKPSTmwFGERTRKTNVIVRTGES------S 231
Cdd:pfam07522   1 PEILSLLTTDpLSTQIHVVPMPKLS----YEALLDYLTARKDHFDSVLAIRPTG--WTYRPPKTEVSDRIGPSirgritI 74

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568912361  232 YRACFSFHSSFSEIKDFLSYICPVNVYPNVIPVG 265
Cdd:pfam07522  75 YGVPYSEHSSFDELKEFVQFLRPKKIIPTVNVGG 108
 
Name Accession Description Interval E-value
artemis-SNM1C-like_MBL-fold cd16297
artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease ...
 3-91 4.24e-57

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: 190.03  E-value: 4.24e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361   3 ITIEIETPTQISLVDEASGEKEEVVVTLLPAGHCPGSVMFLFQGSNGTVLYTGDFRLAKGEASRMELLHSGGRVKDIQSV 82
Cdd:cd16297   83 VSLEIDTPTQISLVDEATGEKEDVVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAVGEAARMELLHSGDRVKDIQSV 162


                 ....*....
gi 568912361  83 YLDTTFCDP 91
Cdd:cd16297  163 YLDTTFCDP 171
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 159-265 9.21e-29

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: 110.44  E-value: 9.21e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361  159 PDILHHLTTD-RNTQIHACRHPKAEecfqWNKLPCGITSQNKTALHTISIKPSTmwFGERTRKTNVIVRTGES------S 231
Cdd:pfam07522   1 PEILSLLTTDpLSTQIHVVPMPKLS----YEALLDYLTARKDHFDSVLAIRPTG--WTYRPPKTEVSDRIGPSirgritI 74

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568912361  232 YRACFSFHSSFSEIKDFLSYICPVNVYPNVIPVG 265
Cdd:pfam07522  75 YGVPYSEHSSFDELKEFVQFLRPKKIIPTVNVGG 108
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 26-111 4.43e-04

RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 42.87  E-value: 4.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361  26 VVVTLLPAGHCPGSVMFLFQGSNGTVLYTGDFrlaKGEASRmeLLHSGGRVKDIQSVYLDTTFCDPRFyqiPSREQCLRG 105
Cdd:COG1236  136 VRVTFHPAGHILGSAQVELEVGGKRIVFSGDY---GREDDP--LLAPPEPVPPADVLITESTYGDRLH---PPREEVEAE 207


                 ....*.
gi 568912361 106 ILELVR 111
Cdd:COG1236  208 LAEWVR 213
 
Name Accession Description Interval E-value
artemis-SNM1C-like_MBL-fold cd16297
artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease ...
 3-91 4.24e-57

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: 190.03  E-value: 4.24e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361   3 ITIEIETPTQISLVDEASGEKEEVVVTLLPAGHCPGSVMFLFQGSNGTVLYTGDFRLAKGEASRMELLHSGGRVKDIQSV 82
Cdd:cd16297   83 VSLEIDTPTQISLVDEATGEKEDVVVTLLPAGHCPGSVMFLFQGNNGTVLYTGDFRLAVGEAARMELLHSGDRVKDIQSV 162


                 ....*....
gi 568912361  83 YLDTTFCDP 91
Cdd:cd16297  163 YLDTTFCDP 171
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 159-265 9.21e-29

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: 110.44  E-value: 9.21e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361  159 PDILHHLTTD-RNTQIHACRHPKAEecfqWNKLPCGITSQNKTALHTISIKPSTmwFGERTRKTNVIVRTGES------S 231
Cdd:pfam07522   1 PEILSLLTTDpLSTQIHVVPMPKLS----YEALLDYLTARKDHFDSVLAIRPTG--WTYRPPKTEVSDRIGPSirgritI 74

                          90       100       110
                  ....*....|....*....|....*....|....
gi 568912361  232 YRACFSFHSSFSEIKDFLSYICPVNVYPNVIPVG 265
Cdd:pfam07522  75 YGVPYSEHSSFDELKEFVQFLRPKKIIPTVNVGG 108
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 5-91 6.45e-24

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: 98.38  E-value: 6.45e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361   5 IEIETPTQISlvdeasgekEEVVVTLLPAGHCPGSVMFLFQGSNG-TVLYTGDFRLAKGEASRMELLHSggrvKDIQSVY 83
Cdd:cd16273   86 LPMNTPVEID---------GDVSVTLLDANHCPGAVMFLFELPDGrRILHTGDFRANPEMLEHPLLLGK----RRIDTVY 152


                 ....*...
gi 568912361  84 LDTTFCDP 91
Cdd:cd16273  153 LDTTYCNP 160
SNM1A-like_MBL-fold cd16298
5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes ...
 26-91 5.88e-12

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: 64.07  E-value: 5.88e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 568912361  26 VVVTLLPAGHCPGSVMFLFQGSNGT-VLYTGDFRLAKGEASRMELLhsGGRvkdIQSVYLDTTFCDP 91
Cdd:cd16298   96 VKVVLLDANHCPGAVMILFRLPSGTlVLHTGDFRADPSMERYPELI--GQK---IHTLYLDTTYCSP 157
TTHA0252-CPSF-like_MBL-fold cd16295
Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; ...
 3-57 6.71e-06

Thermus thermophilus TTHA0252 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain; Includes the archaeal cleavage and polyadenylation specificity factors (CPSFs) such as Methanothermobacter thermautotrophicus MTH1203, and Pyrococcus horikoshii PH1404. In addition to the MBL-fold metallo-hydrolase nuclease and the beta-CASP domains, members of this subgroup contain two contiguous KH domains. 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: 293853 [Multi-domain]  Cd Length: 197  Bit Score: 47.07  E-value: 6.71e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 568912361   3 ITIEIETPTQISlvdeasgekEEVVVTLLPAGHCPGSVMFLFQ-GSNGTVLYTGDF 57
Cdd:cd16295  127 RPVEYGEPFEIG---------PGVKVTFYDAGHILGSASVELEiGGGKRILFSGDL 173
metallo-hydrolase-like_MBL-fold cd07732
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo ...
 19-66 2.73e-04

uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo hydrolase domain; Includes functionally uncharacterized Enterococcus faecalis EF2904. 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, hydroxyacylglutathione hydrolases, AHL (acyl homoserine lactone) lactonases, persulfide dioxygenases, flavodiiron proteins, 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 and ribonuclease Z, cyclic nucleotide phosphodiesterases, insecticide hydrolases, and proteins required for natural transformation competence. Classical members of the superfamily are di-, or less commonly mono-, zinc-ion-dependent hydrolases, however the diversity of biological roles is reflected in variations in the active site metallo-chemistry.


Pssm-ID: 293818 [Multi-domain]  Cd Length: 202  Bit Score: 42.60  E-value: 2.73e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 568912361  19 ASGEKEEV---VVTLLPAGH-CPGSVMFLFQGSNGTVLYTGDFRL--AKGEASR 66
Cdd:cd07732  132 ESGKSFTIgdfTVTPYLVDHsAPGAYAFLIEAPGKRIFYTGDFRFhgRKPELTE 185
YSH1 COG1236
RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure ...
 26-111 4.43e-04

RNA processing exonuclease, beta-lactamase fold, Cft2 family [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440849 [Multi-domain]  Cd Length: 404  Bit Score: 42.87  E-value: 4.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568912361  26 VVVTLLPAGHCPGSVMFLFQGSNGTVLYTGDFrlaKGEASRmeLLHSGGRVKDIQSVYLDTTFCDPRFyqiPSREQCLRG 105
Cdd:COG1236  136 VRVTFHPAGHILGSAQVELEVGGKRIVFSGDY---GREDDP--LLAPPEPVPPADVLITESTYGDRLH---PPREEVEAE 207


                 ....*.
gi 568912361 106 ILELVR 111
Cdd:COG1236  208 LAEWVR 213
Int9-11_CPSF2-3-like_MBL-fold cd07734
Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; ...
 25-57 6.96e-04

Int9, Int11, CPSF2, CPSF3 and related cleavage and polyadenylation specificity factors; MBL-fold metallo-hydrolase domain; CPSF3 (cleavage and polyadenylation specificity factor subunit 3; also known as cleavage and polyadenylation specificity factor 73 kDa subunit, CPSF-73) and CPSF2 (also known as cleavage and polyadenylation specificity factor 100 kDa subunit /CPSF-100) are components of the CPSF complex, which plays a role in 3' end processing of pre-mRNAs during cleavage/polyadenylation, and during processing of metazoan histone pre-mRNAs. CPSF3 functions as a 3' endonuclease. Int11 (also known as cleavage and polyadenylation-specific factor (CPSF) 3-like protein, and protein related to CPSF subunits of 68 kDa (RC-68)), and Int9, also known as protein related to CPSF subunits of 74 kDa (RC-74) are subunits of Integrator, a metazoan-specific multifunctional protein complex composed of 14 subunits. Integrator has been implicated in a variety of Pol II transcription events including 3' end processing of snRNA, transcription initiation, promoter-proximal pausing, termination of protein-coding transcripts, and in HVS pre-miRNA 3' end processing. 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: 293820 [Multi-domain]  Cd Length: 193  Bit Score: 41.16  E-value: 6.96e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 568912361  25 EVVVTLLPAGHCPGSVMFLFQGSNGTVLYTGDF 57
Cdd:cd07734  136 ALSLTAYNAGHVLGAAMWEIQIYGEKLVYTGDF 168
 
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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