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Conserved domains on  [gi|446099915|ref|WP_000177770|]
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RadC family protein [Escherichia coli]

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;
15-149 1.73e-64

DNA repair protein RadC;


The actual alignment was detected with superfamily member PRK00024:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 196.06  E-value: 1.73e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  15 ARDIISRYYQRGVQLCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAA 94
Cdd:PRK00024  89 ARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAA 168

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446099915  95 VILVHNHPSGEPEPSRCDIQLTKKLQELLEILDVRLLDHFIVAGTETVSMAERGL 149
Cdd:PRK00024 169 LILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGL 223
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
15-149 1.73e-64

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 196.06  E-value: 1.73e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  15 ARDIISRYYQRGVQLCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAA 94
Cdd:PRK00024  89 ARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAA 168

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446099915  95 VILVHNHPSGEPEPSRCDIQLTKKLQELLEILDVRLLDHFIVAGTETVSMAERGL 149
Cdd:PRK00024 169 LILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGL 223
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 24-149 5.15e-64

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: 194.89  E-value: 5.15e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  24 QRGVQLCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAVILVHNHPS 103
Cdd:COG2003   98 EERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPS 177

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446099915 104 GEPEPSRCDIQLTKKLQELLEILDVRLLDHFIVAGTETVSMAERGL 149
Cdd:COG2003  178 GDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGL 223
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 29-140 5.07e-56

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: 171.05  E-value: 5.07e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915   29 LCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAVILVHNHPSGEPEP 108
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 446099915  109 SRCDIQLTKKLQELLEILDVRLLDHFIVAGTE 140
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGG 112
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 33-145 6.56e-55

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: 167.94  E-value: 6.56e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  33 DDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAVILVHNHPSGEPEPSRCD 112
Cdd:cd08071    1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446099915 113 IQLTKKLQELLEILDVRLLDHFIVAGTETVSMA 145
Cdd:cd08071   81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 20-150 2.48e-43

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: 142.19  E-value: 2.48e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915   20 SRYYQRGVQ----LCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAV 95
Cdd:TIGR00608  84 KRYAKSRMLerpvIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASAL 163

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446099915   96 ILVHNHPSGEPEPSRCDIQLTKKLQELLEILDVRLLDHFIVAGTETVSMAERGLV 150
Cdd:TIGR00608 164 ILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
15-149 1.73e-64

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 196.06  E-value: 1.73e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  15 ARDIISRYYQRGVQLCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAA 94
Cdd:PRK00024  89 ARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKRALKLNAAA 168

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446099915  95 VILVHNHPSGEPEPSRCDIQLTKKLQELLEILDVRLLDHFIVAGTETVSMAERGL 149
Cdd:PRK00024 169 LILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGL 223
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 24-149 5.15e-64

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: 194.89  E-value: 5.15e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  24 QRGVQLCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAVILVHNHPS 103
Cdd:COG2003   98 EERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIILAHNHPS 177

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 446099915 104 GEPEPSRCDIQLTKKLQELLEILDVRLLDHFIVAGTETVSMAERGL 149
Cdd:COG2003  178 GDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGL 223
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 29-140 5.07e-56

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: 171.05  E-value: 5.07e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915   29 LCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAVILVHNHPSGEPEP 108
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 446099915  109 SRCDIQLTKKLQELLEILDVRLLDHFIVAGTE 140
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGG 112
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 33-145 6.56e-55

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: 167.94  E-value: 6.56e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  33 DDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAVILVHNHPSGEPEPSRCD 112
Cdd:cd08071    1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 446099915 113 IQLTKKLQELLEILDVRLLDHFIVAGTETVSMA 145
Cdd:cd08071   81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 20-150 2.48e-43

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: 142.19  E-value: 2.48e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915   20 SRYYQRGVQ----LCSPDDVRRCVMVELAPLEHEEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKHNAAAV 95
Cdd:TIGR00608  84 KRYAKSRMLerpvIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSASAL 163

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446099915   96 ILVHNHPSGEPEPSRCDIQLTKKLQELLEILDVRLLDHFIVAGTETVSMAERGLV 150
Cdd:TIGR00608 164 ILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 40-136 2.77e-05

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: 40.62  E-value: 2.77e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915  40 MVELAPLEH--EEFGIILLDNHNQLLHREILFRGTLNSVSVHPREVIKRVLKhnaaAVILVHNHPSGEPEPSRCDIQLTK 117
Cdd:cd08059    6 ILVHAKDAHpdEFCGFLSGSKDNVMDELIFLPFVSGSVSAVIDLAALEIGMK----VVGLVHSHPSGSCRPSEADLSLFT 81

                         90
                 ....*....|....*....
gi 446099915 118 KLqelleildvrLLDHFIV 136
Cdd:cd08059   82 RF----------GLYHVIV 90
Prok-JAB pfam14464
Prokaryotic homologs of the JAB domain; These are metalloenzymes that function as the ...
 39-147 6.86e-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: 34.40  E-value: 6.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446099915   39 VMVELAPLEH--EEFGIILLD-NHNQLLHREILFRGTLNSVSVHPREVIKRV---LKHNAAAVILVHNHPSGEPEPSRCD 112
Cdd:pfam14464   7 AIVAHARAAHplECCGILLGNeLESQSVRVIPLVNPMRNRFEIDPGDSLRRVkaaRERGLELVGIYHSHPGGPAYPSETD 86

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 446099915  113 IQltkklqelleiLDVRLLDHFIVAGTETVSMAER 147
Cdd:pfam14464  87 RR-----------DAAGPLPSYVIGGRAPPEIRSW 110
 
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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