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Conserved domains on  [gi|644367560|ref|WP_025304698|]
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MULTISPECIES: DNA repair protein RadC [Serratia]

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;
9-227 7.47e-124

DNA repair protein RadC;


:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 349.76  E-value: 7.47e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   9 WPGALAPREKLLMQGAAALSDAELLAIFLRTGLPGVHVMQLAEQLLRRFGSLYHLMSADHQAFCSQKGLGDASYTQLQAI 88
Cdd:PRK00024   6 WPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560  89 AELALRFFSSHLSQENAMLNPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKAN 168
Cdd:PRK00024  86 LELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 644367560 169 AAALILAHNHPSGKAEPSHADRLITEQVVKACQLLEIRVLDHLVIGRGECVSFAERGWL 227
Cdd:PRK00024 166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
9-227 7.47e-124

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 349.76  E-value: 7.47e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   9 WPGALAPREKLLMQGAAALSDAELLAIFLRTGLPGVHVMQLAEQLLRRFGSLYHLMSADHQAFCSQKGLGDASYTQLQAI 88
Cdd:PRK00024   6 WPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560  89 AELALRFFSSHLSQENAMLNPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKAN 168
Cdd:PRK00024  86 LELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 644367560 169 AAALILAHNHPSGKAEPSHADRLITEQVVKACQLLEIRVLDHLVIGRGECVSFAERGWL 227
Cdd:PRK00024 166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 9-227 1.98e-112

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: 320.85  E-value: 1.98e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   9 WPGALAPREKLLMQGAAALSDAELLAIFLRTGLPGVHVMQLAEQLLRRFGSLYHLMSADHQAFCSQKGLGDASYTQLQAI 88
Cdd:COG2003    6 LPHRERPRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560  89 AELALRFFSSHLSQENAMLNPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKAN 168
Cdd:COG2003   86 LELGRRLLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLN 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 644367560 169 AAALILAHNHPSGKAEPSHADRLITEQVVKACQLLEIRVLDHLVIGRGECVSFAERGWL 227
Cdd:COG2003  166 AAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 15-227 4.11e-92

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: 269.31  E-value: 4.11e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   15 PREKLLMQGAAALSDAELLAIFLRTGLP-GVHVMQLAEQLLRRFG---SLYHLMSADHQAFCSQKGLGDASYTQLQAIAE 90
Cdd:TIGR00608   2 PREKLLKFGAEALSDYELLAIILRTGTPkGLDVLSLSKRLLDVFGrqdSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   91 LALRFFSSHLSQENAMLNPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKANAA 170
Cdd:TIGR00608  82 LAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSAS 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 644367560  171 ALILAHNHPSGKAEPSHADRLITEQVVKACQLLEIRVLDHLVIGRGECVSFAERGWL 227
Cdd:TIGR00608 162 ALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 115-222 1.23e-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: 177.95  E-value: 1.23e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560 115 YLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKANAAALILAHNHPSGKAEPSHADRLITE 194
Cdd:cd08071    6 YLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTK 85

                         90       100
                 ....*....|....*....|....*...
gi 644367560 195 QVVKACQLLEIRVLDHLVIGRGECVSFA 222
Cdd:cd08071   86 RLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 108-217 2.65e-55

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: 172.20  E-value: 2.65e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560  108 NPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKANAAALILAHNHPSGKAEPSH 187
Cdd:pfam04002   3 SPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEPSR 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 644367560  188 ADRLITEQVVKACQLLEIRVLDHLVIGRGE 217
Cdd:pfam04002  83 EDIELTRRLKEAGELLGIRLLDHIIIGDGG 112
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
9-227 7.47e-124

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 349.76  E-value: 7.47e-124
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   9 WPGALAPREKLLMQGAAALSDAELLAIFLRTGLPGVHVMQLAEQLLRRFGSLYHLMSADHQAFCSQKGLGDASYTQLQAI 88
Cdd:PRK00024   6 WPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560  89 AELALRFFSSHLSQENAMLNPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKAN 168
Cdd:PRK00024  86 LELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 644367560 169 AAALILAHNHPSGKAEPSHADRLITEQVVKACQLLEIRVLDHLVIGRGECVSFAERGWL 227
Cdd:PRK00024 166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 9-227 1.98e-112

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: 320.85  E-value: 1.98e-112
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   9 WPGALAPREKLLMQGAAALSDAELLAIFLRTGLPGVHVMQLAEQLLRRFGSLYHLMSADHQAFCSQKGLGDASYTQLQAI 88
Cdd:COG2003    6 LPHRERPRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAA 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560  89 AELALRFFSSHLSQENAMLNPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKAN 168
Cdd:COG2003   86 LELGRRLLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLN 165

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 644367560 169 AAALILAHNHPSGKAEPSHADRLITEQVVKACQLLEIRVLDHLVIGRGECVSFAERGWL 227
Cdd:COG2003  166 AAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 15-227 4.11e-92

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: 269.31  E-value: 4.11e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   15 PREKLLMQGAAALSDAELLAIFLRTGLP-GVHVMQLAEQLLRRFG---SLYHLMSADHQAFCSQKGLGDASYTQLQAIAE 90
Cdd:TIGR00608   2 PREKLLKFGAEALSDYELLAIILRTGTPkGLDVLSLSKRLLDVFGrqdSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560   91 LALRFFSSHLSQENAMLNPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKANAA 170
Cdd:TIGR00608  82 LAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSAS 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 644367560  171 ALILAHNHPSGKAEPSHADRLITEQVVKACQLLEIRVLDHLVIGRGECVSFAERGWL 227
Cdd:TIGR00608 162 ALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 115-222 1.23e-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: 177.95  E-value: 1.23e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560 115 YLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKANAAALILAHNHPSGKAEPSHADRLITE 194
Cdd:cd08071    6 YLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIELTK 85

                         90       100
                 ....*....|....*....|....*...
gi 644367560 195 QVVKACQLLEIRVLDHLVIGRGECVSFA 222
Cdd:cd08071   86 RLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 108-217 2.65e-55

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: 172.20  E-value: 2.65e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560  108 NPRVTQHYLQSLLAHREREVFLVLFLDNQHRVIRHQEMFAGTISSVVVYPREIVREALKANAAALILAHNHPSGKAEPSH 187
Cdd:pfam04002   3 SPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEPSR 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 644367560  188 ADRLITEQVVKACQLLEIRVLDHLVIGRGE 217
Cdd:pfam04002  83 EDIELTRRLKEAGELLGIRLLDHIIIGDGG 112
UPF0758_N pfam20582
UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of ...
 9-77 8.68e-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: 87.72  E-value: 8.68e-23
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 644367560    9 WPGALAPREKLLMQGAAALSDAELLAIFLRTGLPGVHVMQLAEQLLrRFGSLYHLMSADHQAFCSQKGL 77
Cdd:pfam20582   4 WPEDERPREKLLRYGAEALSDAELLAILLGSGTKGESAVDLARRLL-HFGGLRGLLKASVEELMKIKGI 71
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 130-221 5.72e-04

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: 38.31  E-value: 5.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 644367560 130 VLFLDNQHRVIRHQemfAGTISSVVVYPReIVREALKANAAALILAHNHPSGKAEPSHADRliteqvvkacQLLEIRVLD 209
Cdd:cd08059   21 FLSGSKDNVMDELI---FLPFVSGSVSAV-IDLAALEIGMKVVGLVHSHPSGSCRPSEADL----------SLFTRFGLY 86

                         90
                 ....*....|..
gi 644367560 210 HLVIGRGECVSF 221
Cdd:cd08059   87 HVIVCYPYENSW 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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