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Conserved domains on  [gi|1028169776|ref|WP_063918237|]
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DNA repair protein RadC [Serratia surfactantfaciens]

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

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List of domain hits

 Name Accession Description Interval E-value
PRK00024 super family cl31993
DNA repair protein RadC;
19-157 1.54e-57

DNA repair protein RadC;


The actual alignment was detected with superfamily member PRK00024:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 178.73  E-value: 1.54e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  19 RRALslleKYQRQPGEQFTATSFAKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHN 98
Cdd:PRK00024   90 RRIL----AERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1028169776  99 AAAVILAHNHPSGTMEISQQDKYITQRIVKALALVEVRVLDHLVVGGSDVVSFAERGLL 157
Cdd:PRK00024  166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
19-157 1.54e-57

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 178.73  E-value: 1.54e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  19 RRALslleKYQRQPGEQFTATSFAKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHN 98
Cdd:PRK00024   90 RRIL----AERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1028169776  99 AAAVILAHNHPSGTMEISQQDKYITQRIVKALALVEVRVLDHLVVGGSDVVSFAERGLL 157
Cdd:PRK00024  166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 19-157 3.44e-56

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: 175.25  E-value: 3.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  19 RRALslleKYQRQPGEQFTATSFAKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHN 98
Cdd:COG2003    90 RRLL----REELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLN 165

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1028169776  99 AAAVILAHNHPSGTMEISQQDKYITQRIVKALALVEVRVLDHLVVGGSDVVSFAERGLL 157
Cdd:COG2003   166 AAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 42-152 1.72e-51

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: 159.85  E-value: 1.72e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  42 AKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHNAAAVILAHNHPSGTMEISQQDKY 121
Cdd:cd08071     3 VAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIE 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1028169776 122 ITQRIVKALALVEVRVLDHLVVGGSDVVSFA 152
Cdd:cd08071    83 LTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 42-147 1.40e-48

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: 152.17  E-value: 1.40e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  42 AKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHNAAAVILAHNHPSGTMEISQQDKY 121
Cdd:pfam04002   7 VAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEPSREDIE 86

                          90       100
                  ....*....|....*....|....*.
gi 1028169776 122 ITQRIVKALALVEVRVLDHLVVGGSD 147
Cdd:pfam04002  87 LTRRLKEAGELLGIRLLDHIIIGDGG 112
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 42-157 2.75e-42

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: 139.88  E-value: 2.75e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  42 AKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHNAAAVILAHNHPSGTMEISQQDKY 121
Cdd:TIGR00608 103 AAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNHPSGEPSPSQEDIL 182

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1028169776 122 ITQRIVKALALVEVRVLDHLVVGGSDVVSFAERGLL 157
Cdd:TIGR00608 183 ITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
19-157 1.54e-57

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 178.73  E-value: 1.54e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  19 RRALslleKYQRQPGEQFTATSFAKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHN 98
Cdd:PRK00024   90 RRIL----AERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLN 165

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1028169776  99 AAAVILAHNHPSGTMEISQQDKYITQRIVKALALVEVRVLDHLVVGGSDVVSFAERGLL 157
Cdd:PRK00024  166 AAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 19-157 3.44e-56

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: 175.25  E-value: 3.44e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  19 RRALslleKYQRQPGEQFTATSFAKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHN 98
Cdd:COG2003    90 RRLL----REELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLN 165

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1028169776  99 AAAVILAHNHPSGTMEISQQDKYITQRIVKALALVEVRVLDHLVVGGSDVVSFAERGLL 157
Cdd:COG2003   166 AAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 42-152 1.72e-51

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: 159.85  E-value: 1.72e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  42 AKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHNAAAVILAHNHPSGTMEISQQDKY 121
Cdd:cd08071     3 VAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSREDIE 82

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1028169776 122 ITQRIVKALALVEVRVLDHLVVGGSDVVSFA 152
Cdd:cd08071    83 LTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 42-147 1.40e-48

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: 152.17  E-value: 1.40e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  42 AKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHNAAAVILAHNHPSGTMEISQQDKY 121
Cdd:pfam04002   7 VAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEPSREDIE 86

                          90       100
                  ....*....|....*....|....*.
gi 1028169776 122 ITQRIVKALALVEVRVLDHLVVGGSD 147
Cdd:pfam04002  87 LTRRLKEAGELLGIRLLDHIIIGDGG 112
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 42-157 2.75e-42

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: 139.88  E-value: 2.75e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  42 AKSWVQLQLASQEREVFLVMYLDNQHCLLGHETLFMGSISHTEVHPRELVKAALRHNAAAVILAHNHPSGTMEISQQDKY 121
Cdd:TIGR00608 103 AAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASALILAHNHPSGEPSPSQEDIL 182

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1028169776 122 ITQRIVKALALVEVRVLDHLVVGGSDVVSFAERGLL 157
Cdd:TIGR00608 183 ITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 58-151 8.52e-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: 34.07  E-value: 8.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1028169776  58 FLVMYLDNQhcLLGHETLFMGSISHTEVHPrelvKAALRHNAAAVILAHNHPSGTMEISQQDKYITQRIvkalalvevrV 137
Cdd:cd08059    21 FLSGSKDNV--MDELIFLPFVSGSVSAVID----LAALEIGMKVVGLVHSHPSGSCRPSEADLSLFTRF----------G 84

                          90
                  ....*....|....
gi 1028169776 138 LDHLVVGGSDVVSF 151
Cdd:cd08059    85 LYHVIVCYPYENSW 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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