NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2046107516|ref|WP_214174522|]
View 

DNA repair protein RadC [Geomobilimonas luticola]

Protein Classification

Mov34/MPN/PAD-1 family protein( domain architecture ID 1001617)

Mov34/MPN/PAD-1 family protein contains a protein domain of unknown function with 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

Gene Ontology:  GO:0046872|GO:0008237|GO:0006508
PubMed:  18556794|10369758

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK00024 super family cl31993
DNA repair protein RadC;
42-163 2.43e-67

DNA repair protein RadC;


The actual alignment was detected with superfamily member PRK00024:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 204.15  E-value: 2.43e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  42 RFTKPEQVYEMFR-DLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPT 120
Cdd:PRK00024  102 VLLSPEDVADYLMaELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPE 181

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2046107516 121 PSQEDIAITRRLKESGEILGIKVLDHIIVGDDEFLSFVEKGLL 163
Cdd:PRK00024  182 PSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
42-163 2.43e-67

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 204.15  E-value: 2.43e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  42 RFTKPEQVYEMFR-DLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPT 120
Cdd:PRK00024  102 VLLSPEDVADYLMaELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPE 181

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2046107516 121 PSQEDIAITRRLKESGEILGIKVLDHIIVGDDEFLSFVEKGLL 163
Cdd:PRK00024  182 PSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 42-163 5.75e-66

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: 200.67  E-value: 5.75e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  42 RFTKPEQVYEMFR-DLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPT 120
Cdd:COG2003   102 VISSPEDVADYLRaRLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPSGDPE 181

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2046107516 121 PSQEDIAITRRLKESGEILGIKVLDHIIVGDDEFLSFVEKGLL 163
Cdd:COG2003   182 PSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 47-157 1.00e-61

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: 185.66  E-value: 1.00e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  47 EQVYEMFRD-LRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPTPSQED 125
Cdd:cd08071     1 EDVAEYLREeLGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2046107516 126 IAITRRLKESGEILGIKVLDHIIVGDDEFLSF 157
Cdd:cd08071    81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSF 112
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 43-154 4.22e-60

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: 181.83  E-value: 4.22e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  43 FTKPEQVYEMFR-DLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPTP 121
Cdd:pfam04002   1 ITSPEDVAEYLMeELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2046107516 122 SQEDIAITRRLKESGEILGIKVLDHIIVGDDEF 154
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 46-163 3.40e-48

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: 155.29  E-value: 3.40e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  46 PEQVYE-MFRDLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPTPSQE 124
Cdd:TIGR00608 100 PEAAAEfLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNHPSGEPSPSQE 179

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2046107516 125 DIAITRRLKESGEILGIKVLDHIIVGDDEFLSFVEKGLL 163
Cdd:TIGR00608 180 DILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
42-163 2.43e-67

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 204.15  E-value: 2.43e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  42 RFTKPEQVYEMFR-DLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPT 120
Cdd:PRK00024  102 VLLSPEDVADYLMaELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAALILAHNHPSGDPE 181

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2046107516 121 PSQEDIAITRRLKESGEILGIKVLDHIIVGDDEFLSFVEKGLL 163
Cdd:PRK00024  182 PSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 42-163 5.75e-66

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: 200.67  E-value: 5.75e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  42 RFTKPEQVYEMFR-DLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPT 120
Cdd:COG2003   102 VISSPEDVADYLRaRLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPSGDPE 181

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 2046107516 121 PSQEDIAITRRLKESGEILGIKVLDHIIVGDDEFLSFVEKGLL 163
Cdd:COG2003   182 PSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 47-157 1.00e-61

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: 185.66  E-value: 1.00e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  47 EQVYEMFRD-LRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPTPSQED 125
Cdd:cd08071     1 EDVAEYLREeLGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 2046107516 126 IAITRRLKESGEILGIKVLDHIIVGDDEFLSF 157
Cdd:cd08071    81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSF 112
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 43-154 4.22e-60

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: 181.83  E-value: 4.22e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  43 FTKPEQVYEMFR-DLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPTP 121
Cdd:pfam04002   1 ITSPEDVAEYLMeELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 2046107516 122 SQEDIAITRRLKESGEILGIKVLDHIIVGDDEF 154
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 46-163 3.40e-48

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: 155.29  E-value: 3.40e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  46 PEQVYE-MFRDLRRETKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHPREVFKTACLSNAAAILLVHNHPTGDPTPSQE 124
Cdd:TIGR00608 100 PEAAAEfLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNHPSGEPSPSQE 179

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 2046107516 125 DIAITRRLKESGEILGIKVLDHIIVGDDEFLSFVEKGLL 163
Cdd:TIGR00608 180 DILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 60-157 1.47e-09

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: 52.56  E-value: 1.47e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2046107516  60 TKEHFVVLHLDGKNRIVCFDRVSIGSLNQAIVHprevFKTACLSNAAAILLVHNHPTGDPTPSQEDIAITRRLkesgeil 139
Cdd:cd08059    15 PDEFCGFLSGSKDNVMDELIFLPFVSGSVSAVI----DLAALEIGMKVVGLVHSHPSGSCRPSEADLSLFTRF------- 83

                          90
                  ....*....|....*...
gi 2046107516 140 gikVLDHIIVGDDEFLSF 157
Cdd:cd08059    84 ---GLYHVIVCYPYENSW 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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH