MULTISPECIES: DNA repair protein RadC [Rhodanobacter]
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
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||
| PRK00024 | PRK00024 | DNA repair protein RadC; |
1-223 | 1.39e-112 | ||||
DNA repair protein RadC; : Pssm-ID: 178801 [Multi-domain] Cd Length: 224 Bit Score: 321.25 E-value: 1.39e-112
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| Name | Accession | Description | Interval | E-value | ||||
| PRK00024 | PRK00024 | DNA repair protein RadC; |
1-223 | 1.39e-112 | ||||
DNA repair protein RadC; Pssm-ID: 178801 [Multi-domain] Cd Length: 224 Bit Score: 321.25 E-value: 1.39e-112
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| RadC | COG2003 | DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ... |
1-223 | 1.10e-111 | ||||
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: 318.93 E-value: 1.10e-111
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| radc | TIGR00608 | DNA repair protein radc; The genes in this family for which the functions are known have an as ... |
11-223 | 1.36e-69 | ||||
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: 211.91 E-value: 1.36e-69
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| RadC | pfam04002 | RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ... |
102-213 | 4.12e-58 | ||||
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: 179.14 E-value: 4.12e-58
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| MPN_DUF2466 | cd08071 | Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ... |
106-218 | 5.12e-57 | ||||
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: 176.41 E-value: 5.12e-57
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| Name | Accession | Description | Interval | E-value | ||||
| PRK00024 | PRK00024 | DNA repair protein RadC; |
1-223 | 1.39e-112 | ||||
DNA repair protein RadC; Pssm-ID: 178801 [Multi-domain] Cd Length: 224 Bit Score: 321.25 E-value: 1.39e-112
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| RadC | COG2003 | DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ... |
1-223 | 1.10e-111 | ||||
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: 318.93 E-value: 1.10e-111
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| radc | TIGR00608 | DNA repair protein radc; The genes in this family for which the functions are known have an as ... |
11-223 | 1.36e-69 | ||||
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: 211.91 E-value: 1.36e-69
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| RadC | pfam04002 | RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ... |
102-213 | 4.12e-58 | ||||
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: 179.14 E-value: 4.12e-58
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| MPN_DUF2466 | cd08071 | Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ... |
106-218 | 5.12e-57 | ||||
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: 176.41 E-value: 5.12e-57
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| UPF0758_N | pfam20582 | UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of ... |
3-64 | 7.62e-27 | ||||
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: 97.73 E-value: 7.62e-27
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| MPN_prok_mb | cd08059 | Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ... |
110-214 | 1.58e-03 | ||||
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: 36.77 E-value: 1.58e-03
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| Prok-JAB | pfam14464 | Prokaryotic homologs of the JAB domain; These are metalloenzymes that function as the ... |
112-220 | 6.56e-03 | ||||
Prokaryotic homologs of the JAB domain; These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signaling and protein turnover pathways in eukaryotes. Prokaryotic JAB domains are predicted to have a similar role in their cognates of the ubiquitin modification pathway. The domain is widely found in bacteria, archaea and phages where they are present in several gene contexts in addition to those that correspond to the prokaryotic cognates of the eukaryotic Ub pathway. Other contexts in which JAB domains are present include gene neighbor associations with ubiquitin fold domains in cysteine and siderophore biosynthesis, and phage tail morphogenesis, where they are shown or predicted to process the associated ubiquitin. A distinct family, the RadC-like JAB domains are widespread in bacteria and are predicted to function as nucleases. In halophilic archaea the JAB domain shows strong gene-neighborhood associations with a nucleotidyltransferase suggesting a role in nucleotide metabolism. Pssm-ID: 464179 Cd Length: 113 Bit Score: 35.17 E-value: 6.56e-03
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| Blast search parameters | ||||
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