DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, recombination and repair];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2100537542  26 LLERQLREpGASFTSSHAVRDWLRLQLATLEREEFTALFLDNQHRLIAHDTLFTGTINHTQVHPREVVKAALKHNAAAIL 105
Cdd:COG2003    92 LLREELEE-RPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAII 170

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2100537542 106 VAHSHPSGLAEPSDADRRITERLKQALDLVDIRLLDHLVVGGMDIVSFAERGWL 159
Cdd:COG2003   171 LAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2100537542  38 FTSSHAVRDWLRLQLATLEREEFTALFLDNQHRLIAHDTLFTGTINHTQVHPREVVKAALKHNAAAILVAHSHPSGLAEP 117
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2100537542 118 SDADRRITERLKQALDLVDIRLLDHLVVGG 147
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGD 110

DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, recombination and repair];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2100537542  26 LLERQLREpGASFTSSHAVRDWLRLQLATLEREEFTALFLDNQHRLIAHDTLFTGTINHTQVHPREVVKAALKHNAAAIL 105
Cdd:COG2003    92 LLREELEE-RPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAII 170

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2100537542 106 VAHSHPSGLAEPSDADRRITERLKQALDLVDIRLLDHLVVGGMDIVSFAERGWL 159
Cdd:COG2003   171 LAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 224

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2100537542  38 FTSSHAVRDWLRLQLATLEREEFTALFLDNQHRLIAHDTLFTGTINHTQVHPREVVKAALKHNAAAILVAHSHPSGLAEP 117
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 2100537542 118 SDADRRITERLKQALDLVDIRLLDHLVVGG 147
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGD 110

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2100537542  58 EEFTA-LFLDNQHRLIAHDTLFTGTINHTQVHPrevvKAALKHNAAAILVAHSHPSGLAEPSDADRRITERLkqaldlvd 136
Cdd:cd08059    16 DEFCGfLSGSKDNVMDELIFLPFVSGSVSAVID----LAALEIGMKVVGLVHSHPSGSCRPSEADLSLFTRF-------- 83

                          90
                  ....*....|....*..
gi 2100537542 137 irLLDHLVVGGMDIVSF 153
Cdd:cd08059    84 --GLYHVIVCYPYENSW 98

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.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 2100537542  90 REVVKAALKHNAAAILVAHSHPSGLAEPSDADRR 123
Cdd:pfam14464  55 LRRVKAARERGLELVGIYHSHPGGPAYPSETDRR 88

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These 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.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2100537542  89 PRE---VVKAALKHNAAAILVAHSHPSGLAEPSDADRR 123
Cdd:cd08070    55 PAEqlaAQREARERGLEVVGIYHSHPDGPARPSETDLR 92