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 1987858551  20 TIKRALNLLDKYLRQP---GVTFTSAASVRDWLRLQLSPLEREVFMVLFLNNQHQLLAHETLFTGGIRHTEVHPREVLRA 96
Cdd:COG2003    81 QLKAALELGRRLLREEleeRPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKR 160

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1987858551  97 AMHHNAAAVVLAHNHPSGDAEPSQADRLITTRLVNTLELVDIRVLDHFVVGHRDVLSFAERGWL 160
Cdd:COG2003   161 ALRLNAAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 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 1987858551  39 FTSAASVRDWLRLQLSPLEREVFMVLFLNNQHQLLAHETLFTGGIRHTEVHPREVLRAAMHHNAAAVVLAHNHPSGDAEP 118
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1987858551 119 SQADRLITTRLVNTLELVDIRVLDHFVVGHRD 150
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGG 112

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 1987858551  20 TIKRALNLLDKYLRQP---GVTFTSAASVRDWLRLQLSPLEREVFMVLFLNNQHQLLAHETLFTGGIRHTEVHPREVLRA 96
Cdd:COG2003    81 QLKAALELGRRLLREEleeRPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKR 160

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1987858551  97 AMHHNAAAVVLAHNHPSGDAEPSQADRLITTRLVNTLELVDIRVLDHFVVGHRDVLSFAERGWL 160
Cdd:COG2003   161 ALRLNAAAIILAHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEEGLL 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 1987858551  39 FTSAASVRDWLRLQLSPLEREVFMVLFLNNQHQLLAHETLFTGGIRHTEVHPREVLRAAMHHNAAAVVLAHNHPSGDAEP 118
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1987858551 119 SQADRLITTRLVNTLELVDIRVLDHFVVGHRD 150
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGG 112

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 1987858551  63 VLFLNNQHQLLAHETLFTGGIRHTEVHPREVLRAAMHhnaaAVVLAHNHPSGDAEPSQADRLITTRLvntlelvdirVLD 142
Cdd:cd08059    21 FLSGSKDNVMDELIFLPFVSGSVSAVIDLAALEIGMK----VVGLVHSHPSGSCRPSEADLSLFTRF----------GLY 86

                          90
                  ....*....|..
gi 1987858551 143 HFVVGHRDVLSF 154
Cdd:cd08059    87 HVIVCYPYENSW 98

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains; This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein 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        40
                  ....*....|....*....|....*....|....*....|
gi 1987858551  84 RHTEVHPREVLRAAMHHNAAAVVlaHNHPSGDAEPSQADR 123
Cdd:cd08073    43 EHFEISPEDYAAAEDEGEIVAVV--HSHPDGSPAPSEADR 80