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Conserved domains on  [gi|490455318|ref|WP_004326124|]
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MULTISPECIES: RadC family protein [Bacteroidales]

Protein Classification

JAB domain-containing protein( domain architecture ID 11449512)

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
PubMed:  18556794|14737182

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, ...
 13-147 3.26e-42

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: 139.42  E-value: 3.26e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318  13 YKDADASKRVRIHSSKESYDILKTFYEDcmQHHEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGI 92
Cdd:COG2003   92 LLREELEERPVISSPEDVADYLRARLAH--LPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAI 169

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490455318  93 ILSHNHPSGSTVASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSYMDEGML 147
Cdd:COG2003  170 ILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 13-147 3.26e-42

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: 139.42  E-value: 3.26e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318  13 YKDADASKRVRIHSSKESYDILKTFYEDcmQHHEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGI 92
Cdd:COG2003   92 LLREELEERPVISSPEDVADYLRARLAH--LPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAI 169

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490455318  93 ILSHNHPSGSTVASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSYMDEGML 147
Cdd:COG2003  170 ILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 24-138 9.61e-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: 132.14  E-value: 9.61e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318   24 IHSSKESYDILKTFYEDCmqHHEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNHPSGST 103
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDL--DQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDP 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 490455318  104 VASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTY 138
Cdd:pfam04002  79 EPSREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 28-141 1.05e-40

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: 132.11  E-value: 1.05e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318  28 KESYDILKTFYEDCMQhhEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNHPSGSTVAST 107
Cdd:cd08071    1 EDVAEYLREELGDLDQ--EEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSR 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 490455318 108 PDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSY 141
Cdd:cd08071   79 EDIELTKRLKEAGELLGIRLLDHIIVGDGGYFSF 112
PRK00024 PRK00024
DNA repair protein RadC;
21-147 2.07e-28

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 104.00  E-value: 2.07e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318  21 RVRIHSSKESYDILKTFYEDcmQHHEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNHPS 100
Cdd:PRK00024 100 REVLLSPEDVADYLMAELRD--EEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPS 177

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490455318 101 GSTVASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSYMDEGML 147
Cdd:PRK00024 178 GDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 21-147 1.97e-23

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: 90.96  E-value: 1.97e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318   21 RVRIHSSKESYDILKTFYEDCMQH--HEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNH 98
Cdd:TIGR00608  90 RMLERPVIRSPEAAAEFLHTDLAHetREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNH 169

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 490455318   99 PSGSTVASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSYMDEGML 147
Cdd:TIGR00608 170 PSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
 
Name Accession Description Interval E-value
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 13-147 3.26e-42

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: 139.42  E-value: 3.26e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318  13 YKDADASKRVRIHSSKESYDILKTFYEDcmQHHEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGI 92
Cdd:COG2003   92 LLREELEERPVISSPEDVADYLRARLAH--LPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAI 169

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 490455318  93 ILSHNHPSGSTVASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSYMDEGML 147
Cdd:COG2003  170 ILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 24-138 9.61e-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: 132.14  E-value: 9.61e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318   24 IHSSKESYDILKTFYEDCmqHHEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNHPSGST 103
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDL--DQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDP 78

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 490455318  104 VASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTY 138
Cdd:pfam04002  79 EPSREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 28-141 1.05e-40

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: 132.11  E-value: 1.05e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318  28 KESYDILKTFYEDCMQhhEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNHPSGSTVAST 107
Cdd:cd08071    1 EDVAEYLREELGDLDQ--EEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSR 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 490455318 108 PDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSY 141
Cdd:cd08071   79 EDIELTKRLKEAGELLGIRLLDHIIVGDGGYFSF 112
PRK00024 PRK00024
DNA repair protein RadC;
21-147 2.07e-28

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 104.00  E-value: 2.07e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318  21 RVRIHSSKESYDILKTFYEDcmQHHEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNHPS 100
Cdd:PRK00024 100 REVLLSPEDVADYLMAELRD--EEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPS 177

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 490455318 101 GSTVASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSYMDEGML 147
Cdd:PRK00024 178 GDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 21-147 1.97e-23

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: 90.96  E-value: 1.97e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490455318   21 RVRIHSSKESYDILKTFYEDCMQH--HEECWAMYLNGAGRLLGVSCVSRSGMNSTVVDIRIVLQTALVSHASGIILSHNH 98
Cdd:TIGR00608  90 RMLERPVIRSPEAAAEFLHTDLAHetREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNH 169

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 490455318   99 PSGSTVASTPDNNLTSQLKKGCEAIGIQLLDHIILTEDTYLSYMDEGML 147
Cdd:TIGR00608 170 PSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
 
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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