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Conserved domains on  [gi|379647935|gb|AFD04904|]
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DNA repair protein [Treponema denticola]

Protein Classification

RadC family protein( domain architecture ID 11449512)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 15-220 6.47e-79

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: 236.11  E-value: 6.47e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  15 MRERLLEYGPQNLSDSDLVAILLRTGIKDKPVKELADDIILHID------RARPEKiegyLRSIRGMGDSKISTVLAALE 88
Cdd:COG2003   12 PRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGslrgllRASVEE----LRKIKGIGEAKAAQLKAALE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  89 LGRRYYD---NKNRTISHPTDVVPLLQ-HYADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDRAA 164
Cdd:COG2003   88 LGRRLLReelEERPVISSPEDVADYLRaRLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAA 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 379647935 165 AIIAAHNHPSGNLEPSSEDMELTKRIYEAGKILGIKLLDHIIlVPNGNFFSFVQSG 220
Cdd:COG2003  168 AIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHII-IGDGGYVSFAEEG 222
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 15-220 6.47e-79

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: 236.11  E-value: 6.47e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  15 MRERLLEYGPQNLSDSDLVAILLRTGIKDKPVKELADDIILHID------RARPEKiegyLRSIRGMGDSKISTVLAALE 88
Cdd:COG2003   12 PRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGslrgllRASVEE----LRKIKGIGEAKAAQLKAALE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  89 LGRRYYD---NKNRTISHPTDVVPLLQ-HYADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDRAA 164
Cdd:COG2003   88 LGRRLLReelEERPVISSPEDVADYLRaRLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAA 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 379647935 165 AIIAAHNHPSGNLEPSSEDMELTKRIYEAGKILGIKLLDHIIlVPNGNFFSFVQSG 220
Cdd:COG2003  168 AIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHII-IGDGGYVSFAEEG 222
PRK00024 PRK00024
DNA repair protein RadC;
16-220 3.33e-73

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 221.49  E-value: 3.33e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  16 RERLLEYGPQNLSDSDLVAILLRTGIKDKPVKELADDII---------LHIDRARpekiegyLRSIRGMGDSKISTVLAA 86
Cdd:PRK00024  13 RERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLqrfgslrglLDASLEE-------LQSIKGIGPAKAAQLKAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  87 LELGRRYY--DNKNRT-ISHPTDVVPLLQHY-ADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDR 162
Cdd:PRK00024  86 LELARRILaeRLREREvLLSPEDVADYLMAElRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 379647935 163 AAAIIAAHNHPSGNLEPSSEDMELTKRIYEAGKILGIKLLDHIIlVPNGNFFSFVQSG 220
Cdd:PRK00024 166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHII-IGDGEYVSFAERG 222
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 16-220 5.23e-55

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: 174.93  E-value: 5.23e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935   16 RERLLEYGPQNLSDSDLVAILLRTGIKDK-PVKELADDIILHIDR---------ARPEKiegyLRSIRGMGDSKISTVLA 85
Cdd:TIGR00608   3 REKLLKFGAEALSDYELLAIILRTGTPKGlDVLSLSKRLLDVFGRqdslghllsAPPEE----LSSVPGIGEAKAIQLKA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935   86 ALELGRRYYDNKNRT---ISHPTDVVPLL-QHYADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKD 161
Cdd:TIGR00608  79 AVELAKRYAKSRMLErpvIRSPEAAAEFLhTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKL 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 379647935  162 RAAAIIAAHNHPSGNLEPSSEDMELTKRIYEAGKILGIKLLDHIILvPNGNFFSFVQSG 220
Cdd:TIGR00608 159 SASALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLII-GKGRYVSFREEG 216
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 110-216 4.95e-44

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: 143.29  E-value: 4.95e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935 110 LLQHYADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDRAAAIIAAHNHPSGNLEPSSEDMELTKR 189
Cdd:cd08071    7 LREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKR 86

                         90       100
                 ....*....|....*....|....*..
gi 379647935 190 IYEAGKILGIKLLDHIIlVPNGNFFSF 216
Cdd:cd08071   87 LKEAGELLGIRLLDHII-VGDGGYFSF 112
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 101-206 1.43e-41

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: 137.15  E-value: 1.43e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  101 ISHPTDVVPLLQHY-ADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDRAAAIIAAHNHPSGNLEP 179
Cdd:pfam04002   1 ITSPEDVAEYLMEElRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100
                  ....*....|....*....|....*..
gi 379647935  180 SSEDMELTKRIYEAGKILGIKLLDHII 206
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHII 107
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 15-220 6.47e-79

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: 236.11  E-value: 6.47e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  15 MRERLLEYGPQNLSDSDLVAILLRTGIKDKPVKELADDIILHID------RARPEKiegyLRSIRGMGDSKISTVLAALE 88
Cdd:COG2003   12 PRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGslrgllRASVEE----LRKIKGIGEAKAAQLKAALE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  89 LGRRYYD---NKNRTISHPTDVVPLLQ-HYADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDRAA 164
Cdd:COG2003   88 LGRRLLReelEERPVISSPEDVADYLRaRLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAA 167

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 379647935 165 AIIAAHNHPSGNLEPSSEDMELTKRIYEAGKILGIKLLDHIIlVPNGNFFSFVQSG 220
Cdd:COG2003  168 AIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHII-IGDGGYVSFAEEG 222
PRK00024 PRK00024
DNA repair protein RadC;
16-220 3.33e-73

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 221.49  E-value: 3.33e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  16 RERLLEYGPQNLSDSDLVAILLRTGIKDKPVKELADDII---------LHIDRARpekiegyLRSIRGMGDSKISTVLAA 86
Cdd:PRK00024  13 RERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLqrfgslrglLDASLEE-------LQSIKGIGPAKAAQLKAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  87 LELGRRYY--DNKNRT-ISHPTDVVPLLQHY-ADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDR 162
Cdd:PRK00024  86 LELARRILaeRLREREvLLSPEDVADYLMAElRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 379647935 163 AAAIIAAHNHPSGNLEPSSEDMELTKRIYEAGKILGIKLLDHIIlVPNGNFFSFVQSG 220
Cdd:PRK00024 166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHII-IGDGEYVSFAERG 222
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 16-220 5.23e-55

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: 174.93  E-value: 5.23e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935   16 RERLLEYGPQNLSDSDLVAILLRTGIKDK-PVKELADDIILHIDR---------ARPEKiegyLRSIRGMGDSKISTVLA 85
Cdd:TIGR00608   3 REKLLKFGAEALSDYELLAIILRTGTPKGlDVLSLSKRLLDVFGRqdslghllsAPPEE----LSSVPGIGEAKAIQLKA 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935   86 ALELGRRYYDNKNRT---ISHPTDVVPLL-QHYADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKD 161
Cdd:TIGR00608  79 AVELAKRYAKSRMLErpvIRSPEAAAEFLhTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKL 158

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 379647935  162 RAAAIIAAHNHPSGNLEPSSEDMELTKRIYEAGKILGIKLLDHIILvPNGNFFSFVQSG 220
Cdd:TIGR00608 159 SASALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLII-GKGRYVSFREEG 216
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 110-216 4.95e-44

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: 143.29  E-value: 4.95e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935 110 LLQHYADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDRAAAIIAAHNHPSGNLEPSSEDMELTKR 189
Cdd:cd08071    7 LREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTKR 86

                         90       100
                 ....*....|....*....|....*..
gi 379647935 190 IYEAGKILGIKLLDHIIlVPNGNFFSF 216
Cdd:cd08071   87 LKEAGELLGIRLLDHII-VGDGGYFSF 112
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 101-206 1.43e-41

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: 137.15  E-value: 1.43e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935  101 ISHPTDVVPLLQHY-ADRDREHFICVSLNGANEIIATRVVSVGTINRTIVHPREVYSDPLKDRAAAIIAAHNHPSGNLEP 179
Cdd:pfam04002   1 ITSPEDVAEYLMEElRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100
                  ....*....|....*....|....*..
gi 379647935  180 SSEDMELTKRIYEAGKILGIKLLDHII 206
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHII 107
UPF0758_N pfam20582
UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of ...
 11-75 2.29e-13

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: 62.68  E-value: 2.29e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 379647935   11 DKPdmRERLLEYGPQNLSDSDLVAILLRTGIKDKPVKELADDIILH-----IDRARPEKiegyLRSIRGM 75
Cdd:pfam20582   8 ERP--REKLLRYGAEALSDAELLAILLGSGTKGESAVDLARRLLHFgglrgLLKASVEE----LMKIKGI 71
 
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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