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Conserved domains on  [gi|495040515|ref|WP_007765544|]
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MULTISPECIES: DNA repair protein RadC [Cronobacter]

Protein Classification

JAB domain-containing protein( domain architecture ID 11477685)

JAB or Mpr1p, Pad1p N-terminal (MPN) domain-containing protein contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, which is involved in zinc ion coordination; a function as a nuclease has been suggested

Gene Ontology:  GO:0046872|GO:0008237|GO:0006508

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
8-220 2.18e-123

DNA repair protein RadC;


:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 348.22  E-value: 2.18e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   8 PREKLMRYGAADLSDEELLAIFLRTGTPGMDVMTLAKRLLAHFGSLYGLLSADIAPFRQIGGVGMAKYVQLRAIGELARR 87
Cdd:PRK00024  12 PRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALELARR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515  88 YYRSRPNEETALLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIIL 167
Cdd:PRK00024  92 ILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALIL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495040515 168 AHNHPSGHAEPSRADKMVTERIVKCCQLVDIRVLDHLVIGRGEYVSFAERGWI 220
Cdd:PRK00024 172 AHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
8-220 2.18e-123

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 348.22  E-value: 2.18e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   8 PREKLMRYGAADLSDEELLAIFLRTGTPGMDVMTLAKRLLAHFGSLYGLLSADIAPFRQIGGVGMAKYVQLRAIGELARR 87
Cdd:PRK00024  12 PRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALELARR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515  88 YYRSRPNEETALLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIIL 167
Cdd:PRK00024  92 ILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALIL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495040515 168 AHNHPSGHAEPSRADKMVTERIVKCCQLVDIRVLDHLVIGRGEYVSFAERGWI 220
Cdd:PRK00024 172 AHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 8-220 3.06e-116

DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, recombination and repair];


Pssm-ID: 441606 [Multi-domain]  Cd Length: 224  Bit Score: 330.48  E-value: 3.06e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   8 PREKLMRYGAADLSDEELLAIFLRTGTPGMDVMTLAKRLLAHFGSLYGLLSADIAPFRQIGGVGMAKYVQLRAIGELARR 87
Cdd:COG2003   12 PRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAALELGRR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515  88 YYRSRPNEETALLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIIL 167
Cdd:COG2003   92 LLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIIL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495040515 168 AHNHPSGHAEPSRADKMVTERIVKCCQLVDIRVLDHLVIGRGEYVSFAERGWI 220
Cdd:COG2003  172 AHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 8-220 1.11e-100

DNA repair protein radc; The genes in this family for which the functions are known have an as yet porrly defined role in determining sensitivity to DNA damaging agents such as UV irradiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273171 [Multi-domain]  Cd Length: 218  Bit Score: 290.88  E-value: 1.11e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515    8 PREKLMRYGAADLSDEELLAIFLRTGTP-GMDVMTLAKRLLAHFG---SLYGLLSADIAPFRQIGGVGMAKYVQLRAIGE 83
Cdd:TIGR00608   2 PREKLLKFGAEALSDYELLAIILRTGTPkGLDVLSLSKRLLDVFGrqdSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   84 LARRYYRSRPNEETALLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAA 163
Cdd:TIGR00608  82 LAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSAS 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 495040515  164 GIILAHNHPSGHAEPSRADKMVTERIVKCCQLVDIRVLDHLVIGRGEYVSFAERGWI 220
Cdd:TIGR00608 162 ALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 106-215 1.09e-59

Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.


Pssm-ID: 163702  Cd Length: 113  Bit Score: 182.96  E-value: 1.09e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515 106 REFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIILAHNHPSGHAEPSRADKMV 185
Cdd:cd08071    4 AEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIEL 83

                         90       100       110
                 ....*....|....*....|....*....|
gi 495040515 186 TERIVKCCQLVDIRVLDHLVIGRGEYVSFA 215
Cdd:cd08071   84 TKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 99-211 4.19e-56

RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions. However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG. In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterize a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily of metalloproteins. The domain shows fusions to an N-terminal Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the same position as the RadC-like JAB domain. These conserved domain associations lead to the hypothesis that the RadC-like JAB domains might function as a nuclease.


Pssm-ID: 461124  Cd Length: 113  Bit Score: 173.74  E-value: 4.19e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   99 LLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIILAHNHPSGHAEP 178
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 495040515  179 SRADKMVTERIVKCCQLVDIRVLDHLVIGRGEY 211
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
8-220 2.18e-123

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 348.22  E-value: 2.18e-123
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   8 PREKLMRYGAADLSDEELLAIFLRTGTPGMDVMTLAKRLLAHFGSLYGLLSADIAPFRQIGGVGMAKYVQLRAIGELARR 87
Cdd:PRK00024  12 PRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAALELARR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515  88 YYRSRPNEETALLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIIL 167
Cdd:PRK00024  92 ILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALIL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495040515 168 AHNHPSGHAEPSRADKMVTERIVKCCQLVDIRVLDHLVIGRGEYVSFAERGWI 220
Cdd:PRK00024 172 AHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 8-220 3.06e-116

DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, recombination and repair];


Pssm-ID: 441606 [Multi-domain]  Cd Length: 224  Bit Score: 330.48  E-value: 3.06e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   8 PREKLMRYGAADLSDEELLAIFLRTGTPGMDVMTLAKRLLAHFGSLYGLLSADIAPFRQIGGVGMAKYVQLRAIGELARR 87
Cdd:COG2003   12 PRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAALELGRR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515  88 YYRSRPNEETALLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIIL 167
Cdd:COG2003   92 LLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIIL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 495040515 168 AHNHPSGHAEPSRADKMVTERIVKCCQLVDIRVLDHLVIGRGEYVSFAERGWI 220
Cdd:COG2003  172 AHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 8-220 1.11e-100

DNA repair protein radc; The genes in this family for which the functions are known have an as yet porrly defined role in determining sensitivity to DNA damaging agents such as UV irradiation. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273171 [Multi-domain]  Cd Length: 218  Bit Score: 290.88  E-value: 1.11e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515    8 PREKLMRYGAADLSDEELLAIFLRTGTP-GMDVMTLAKRLLAHFG---SLYGLLSADIAPFRQIGGVGMAKYVQLRAIGE 83
Cdd:TIGR00608   2 PREKLLKFGAEALSDYELLAIILRTGTPkGLDVLSLSKRLLDVFGrqdSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   84 LARRYYRSRPNEETALLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAA 163
Cdd:TIGR00608  82 LAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSAS 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 495040515  164 GIILAHNHPSGHAEPSRADKMVTERIVKCCQLVDIRVLDHLVIGRGEYVSFAERGWI 220
Cdd:TIGR00608 162 ALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 106-215 1.09e-59

Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of unknown function contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. However, to date, the name RadC has been misleading and no function has been determined.


Pssm-ID: 163702  Cd Length: 113  Bit Score: 182.96  E-value: 1.09e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515 106 REFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIILAHNHPSGHAEPSRADKMV 185
Cdd:cd08071    4 AEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIEL 83

                         90       100       110
                 ....*....|....*....|....*....|
gi 495040515 186 TERIVKCCQLVDIRVLDHLVIGRGEYVSFA 215
Cdd:cd08071   84 TKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 99-211 4.19e-56

RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was named initially with reference to the E. coli radC102 mutation which suggested that RadC was involved in repair of DNA lesions. However the relevant mutation has subsequently been shown to be in recG, where radC is in fact an allele of recG. In addition, a personal communication from Claverys, J-P, et al, indicates a total failure of all attempts to characterize a radiation-related function for RadC in Streptococcus pneumoniae, suggesting that it is not involved in repair of DNA lesions, in recombination during transformation, in gene conversion, nor in mismatch repair. Computational analysis, however, provides a possible function. The RadC-like family belong to the JAB superfamily of metalloproteins. The domain shows fusions to an N-terminal Helix-hairpin-Helix (HhH) domain in most instances. Other domain combinations include fusions to the anti-restriction module ArdC, the DinG/RAD3-like superfamily II helicases and the DNAG-like primase. In some bacteria, closely related DinG/Rad3- like superfamily II helicases are fused to a 3'-5' exonuclease in the same position as the RadC-like JAB domain. These conserved domain associations lead to the hypothesis that the RadC-like JAB domains might function as a nuclease.


Pssm-ID: 461124  Cd Length: 113  Bit Score: 173.74  E-value: 4.19e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515   99 LLSPTITREFLESQLAEQEREMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREIVREAVRLNAAGIILAHNHPSGHAEP 178
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 495040515  179 SRADKMVTERIVKCCQLVDIRVLDHLVIGRGEY 211
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
UPF0758_N pfam20582
UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of ...
 8-70 2.48e-23

UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of the uncharacterized UPF0758 proteins from bacteria and archaea, and is approximately 90 amino acids in length. UPF0758 was previously known as the radC family, a name that was assigned according to the radC102 mutant of E. coli which was later demonstrated to be an allele of the transcription-repair-coupling factor recG. UPF0758 has been described as a putative JAMM-family deubiquitinating enzyme, but its function remains to be determined. Structure prediction using Colab notebook from AlphaFold DB suggests that it has an alpha bundle fold. It may contain two helix-hairpin-helix (HhH) motifs. This domain is found in association with pfam04002.


Pssm-ID: 466731 [Multi-domain]  Cd Length: 71  Bit Score: 88.87  E-value: 2.48e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 495040515    8 PREKLMRYGAADLSDEELLAIFLRTGTPGMDVMTLAKRLLaHFGSLYGLLSADIAPFRQIGGV 70
Cdd:pfam20582  10 PREKLLRYGAEALSDAELLAILLGSGTKGESAVDLARRLL-HFGGLRGLLKASVEELMKIKGI 71
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 119-214 2.03e-05

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic; This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163690  Cd Length: 101  Bit Score: 42.16  E-value: 2.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495040515 119 EMFLVIFLDSQNRIIRQNTLFTGTLSHVEVHPREivreAVRLNAAGIILAHNHPSGHAEPSRADKmvterivkccQLVDI 198
Cdd:cd08059   17 EFCGFLSGSKDNVMDELIFLPFVSGSVSAVIDLA----ALEIGMKVVGLVHSHPSGSCRPSEADL----------SLFTR 82

                         90
                 ....*....|....*.
gi 495040515 199 RVLDHLVIGRGEYVSF 214
Cdd:cd08059   83 FGLYHVIVCYPYENSW 98
 
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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