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Conserved domains on  [gi|1958643026|ref|XP_038959100|]
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DNA cross-link repair 1A protein isoform X2 [Rattus norvegicus]

Protein Classification

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

DNA cross-link repair protein similar to Mus musculus DNA cross-link repair 1A protein that may be required for DNA interstrand cross-link repair, and also required for checkpoint mediated cell cycle arrest in early prophase in response to mitotic spindle poisons

CATH:  3.40.50.12650|3.60.15.10
Gene Ontology:  GO:0003684|GO:0046872|GO:0006281|GO:0035312|GO:0036297
PubMed:  12177301|20528238|11471246|11513844|17597585

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; ...
 675-778 1.38e-63

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 cd16298:

Pssm-ID: 451500 [Multi-domain]  Cd Length: 157  Bit Score: 211.61  E-value: 1.38e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958643026 675 SESSGGGESRRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTRPIYCSEITGSLLKKKLRVQEQ 754
Cdd:cd16298     1 SSTNGEGKRKKTCPFYKKIPGTGFTVDAFQYGVIEGCTAYFLTHFHSDHYCGLTKKFKFPIYCSKITGNLVKSKLKVEEQ 80

                          90       100
                  ....*....|....*....|....
gi 1958643026 755 YIHQLPMDTECIVDGVKVVLLDAN 778
Cdd:cd16298    81 YINVLPMNTECIVNGVKVVLLDAN 104
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 853-958 1.51e-47

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: 164.76  E-value: 1.51e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958643026 853 PEVSSLITTDMCNSLVHLLPMMQINFKGLQNHLKKCGGKFDQILAFRPTGWTHSNNITS-IADITPQTKGNIAIYGIPYS 931
Cdd:pfam07522   1 PEILSLLTTDPLSTQIHVVPMPKLSYEALLDYLTARKDHFDSVLAIRPTGWTYRPPKTEvSDRIGPSIRGRITIYGVPYS 80

                          90       100
                  ....*....|....*....|....*..
gi 1958643026 932 EHSSYLEMKRFVQWLKPQKIIPTVNVG 958
Cdd:pfam07522  81 EHSSFDELKEFVQFLRPKKIIPTVNVG 107
 
Name Accession Description Interval E-value
SNM1A-like_MBL-fold cd16298
5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes ...
 675-778 1.38e-63

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: 211.61  E-value: 1.38e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958643026 675 SESSGGGESRRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTRPIYCSEITGSLLKKKLRVQEQ 754
Cdd:cd16298     1 SSTNGEGKRKKTCPFYKKIPGTGFTVDAFQYGVIEGCTAYFLTHFHSDHYCGLTKKFKFPIYCSKITGNLVKSKLKVEEQ 80

                          90       100
                  ....*....|....*....|....
gi 1958643026 755 YIHQLPMDTECIVDGVKVVLLDAN 778
Cdd:cd16298    81 YINVLPMNTECIVNGVKVVLLDAN 104
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 853-958 1.51e-47

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: 164.76  E-value: 1.51e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958643026 853 PEVSSLITTDMCNSLVHLLPMMQINFKGLQNHLKKCGGKFDQILAFRPTGWTHSNNITS-IADITPQTKGNIAIYGIPYS 931
Cdd:pfam07522   1 PEILSLLTTDPLSTQIHVVPMPKLSYEALLDYLTARKDHFDSVLAIRPTGWTYRPPKTEvSDRIGPSIRGRITIYGVPYS 80

                          90       100
                  ....*....|....*....|....*..
gi 1958643026 932 EHSSYLEMKRFVQWLKPQKIIPTVNVG 958
Cdd:pfam07522  81 EHSSFDELKEFVQFLRPKKIIPTVNVG 107
PhnP COG1235
Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]; ...
 715-778 1.58e-04

Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism];


Pssm-ID: 440848 [Multi-domain]  Cd Length: 259  Bit Score: 44.50  E-value: 1.58e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958643026 715 FLTHFHSDHYAGLsKDFTR-------PIYCSEITGSLLKKKLRVQEQY------IHQLPMDTECIVDGVKVVLLDAN 778
Cdd:COG1235    73 LLTHEHADHIAGL-DDLRPrygpnpiPVYATPGTLEALERRFPYLFAPypgkleFHEIEPGEPFEIGGLTVTPFPVP 148
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 715-776 4.50e-03

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 39.07  E-value: 4.50e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958643026  715 FLTHFHSDHYAG---LSKDFTRPIYCSEITGSLLKKKLRVQEQYIHQLPM--DTECIVDGVKVVLLD 776
Cdd:smart00849  40 ILTHGHPDHIGGlpeLLEAPGAPVYAPEGTAELLKDLLALLGELGAEAEPapPDRTLKDGDELDLGG 106
 
Name Accession Description Interval E-value
SNM1A-like_MBL-fold cd16298
5'-exonucleases human SNM1A and related proteins; MBL-fold metallo-hydrolase domain; Includes ...
 675-778 1.38e-63

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: 211.61  E-value: 1.38e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958643026 675 SESSGGGESRRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTRPIYCSEITGSLLKKKLRVQEQ 754
Cdd:cd16298     1 SSTNGEGKRKKTCPFYKKIPGTGFTVDAFQYGVIEGCTAYFLTHFHSDHYCGLTKKFKFPIYCSKITGNLVKSKLKVEEQ 80

                          90       100
                  ....*....|....*....|....
gi 1958643026 755 YIHQLPMDTECIVDGVKVVLLDAN 778
Cdd:cd16298    81 YINVLPMNTECIVNGVKVVLLDAN 104
SNM1A-1C-like_MBL-fold cd16273
SNM1A , artemis/SNM1C, yeast Pso2p, and related proteins; MBL-fold metallo-hydrolase domain; ...
 684-778 6.45e-52

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: 179.27  E-value: 6.45e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958643026 684 RRTCPFYKRIPGTGFTVDAFQYGEIEGCTAYFLTHFHSDHYAGLSKDFTR-PIYCSEITGSLLKKKLRVQEQYIHQLPMD 762
Cdd:cd16273    10 KKPCPFYKIIPGTSFVVDAFKYGKIPGISAYFLSHFHSDHYGGLTKSWSHgPIYCSEITANLVKLKLKVDEEYIVVLPMN 89

                          90
                  ....*....|....*..
gi 1958643026 763 TEC-IVDGVKVVLLDAN 778
Cdd:cd16273    90 TPVeIDGDVSVTLLDAN 106
DRMBL pfam07522
DNA repair metallo-beta-lactamase; The metallo-beta-lactamase fold contains five sequence ...
 853-958 1.51e-47

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: 164.76  E-value: 1.51e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958643026 853 PEVSSLITTDMCNSLVHLLPMMQINFKGLQNHLKKCGGKFDQILAFRPTGWTHSNNITS-IADITPQTKGNIAIYGIPYS 931
Cdd:pfam07522   1 PEILSLLTTDPLSTQIHVVPMPKLSYEALLDYLTARKDHFDSVLAIRPTGWTYRPPKTEvSDRIGPSIRGRITIYGVPYS 80

                          90       100
                  ....*....|....*....|....*..
gi 1958643026 932 EHSSYLEMKRFVQWLKPQKIIPTVNVG 958
Cdd:pfam07522  81 EHSSFDELKEFVQFLRPKKIIPTVNVG 107
PhnP COG1235
Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism]; ...
 715-778 1.58e-04

Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [Inorganic ion transport and metabolism];


Pssm-ID: 440848 [Multi-domain]  Cd Length: 259  Bit Score: 44.50  E-value: 1.58e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958643026 715 FLTHFHSDHYAGLsKDFTR-------PIYCSEITGSLLKKKLRVQEQY------IHQLPMDTECIVDGVKVVLLDAN 778
Cdd:COG1235    73 LLTHEHADHIAGL-DDLRPrygpnpiPVYATPGTLEALERRFPYLFAPypgkleFHEIEPGEPFEIGGLTVTPFPVP 148
artemis-SNM1C-like_MBL-fold cd16297
artemis-SNM1C and related proteins; MBL-fold metallo-hydrolase domain; Includes the nuclease ...
 699-763 3.55e-04

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: 42.49  E-value: 3.55e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1958643026 699 TVDAFQYGEIEGcTAYFLTHFHSDHYAGLSKDFTRP---------IYCSEITGSLL--KKKLRVQEQYIHQLPMDT 763
Cdd:cd16297    15 SIDRFDRENLRA-RAYFLSHCHKDHMKGLRAPGLKRrlkaslkvkLYCSPVTKELLltNPKYAFWENHIVSLEIDT 89
RnjA COG0595
mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];
713-750 7.73e-04

mRNA degradation ribonuclease J1/J2 [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440360 [Multi-domain]  Cd Length: 553  Bit Score: 43.13  E-value: 7.73e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958643026 713 AYFLTHFHSDHYAGLS---KDFTRPIYCSEITGSLLKKKLR 750
Cdd:COG0595    66 GIVLTHGHEDHIGALPyllKELNVPVYGTPLTLALLEAKLK 106
metallo-hydrolase-like_MBL-fold cd07732
uncharacterized subgroup of the MBL-fold_metallo-hydrolase superfamily; MBL-fold metallo ...
 693-746 2.14e-03

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: 40.29  E-value: 2.14e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1958643026 693 IPGTGFTVDAFQYGEIEG---CTAYFLTHFHSDHYAGLSK-DFTRPIYCSEITGSLLK 746
Cdd:cd07732    55 IVGLYRDPLLLGGLRSEEdpsVDAVLLSHAHLDHYGLLNYlRPDIPVYMGEATKRILK 112
Lactamase_B smart00849
Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins ...
 715-776 4.50e-03

Metallo-beta-lactamase superfamily; Apart from the beta-lactamases a number of other proteins contain this domain. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.


Pssm-ID: 214854 [Multi-domain]  Cd Length: 177  Bit Score: 39.07  E-value: 4.50e-03
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958643026  715 FLTHFHSDHYAG---LSKDFTRPIYCSEITGSLLKKKLRVQEQYIHQLPM--DTECIVDGVKVVLLD 776
Cdd:smart00849  40 ILTHGHPDHIGGlpeLLEAPGAPVYAPEGTAELLKDLLALLGELGAEAEPapPDRTLKDGDELDLGG 106
 
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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