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Conserved domains on  [gi|636879336|ref|WP_024385285|]
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MULTISPECIES: RadC family protein [Streptococcus]

Protein Classification

JAB domain-containing protein( domain architecture ID 11477685)

JAB or Mpr1p, Pad1p N-terminal (MPN) domain-containing protein that contains the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, which is involved in zinc ion coordination; similar to UPF0758 protein YicR

CATH:  3.40.140.10
Gene Ontology:  GO:0046872
PubMed:  14737182|18556794
SCOP:  4004298

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
2-225 7.88e-107

DNA repair protein RadC;


:

Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 306.62  E-value: 7.88e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336   2 YQIEFKEEATLPRERLVEVGAERLSNQELLAIFIRTGTKKEPVSILSNKLLNRLESLAALRELSIEELQSLTGIGRVKAI 81
Cdd:PRK00024   1 MRIKDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  82 EIKAMIELGKRINQSELLLNERILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHY 161
Cdd:PRK00024  81 QLKAALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKR 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 636879336 162 AVKCMATSIIIVHNHPSGSVQPSRNDLLFTENLKESCEKLGLVLLDHLIVGNKDYYSFREESEL 225
Cdd:PRK00024 161 ALKLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
2-225 7.88e-107

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 306.62  E-value: 7.88e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336   2 YQIEFKEEATLPRERLVEVGAERLSNQELLAIFIRTGTKKEPVSILSNKLLNRLESLAALRELSIEELQSLTGIGRVKAI 81
Cdd:PRK00024   1 MRIKDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  82 EIKAMIELGKRINQSELLLNERILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHY 161
Cdd:PRK00024  81 QLKAALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKR 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 636879336 162 AVKCMATSIIIVHNHPSGSVQPSRNDLLFTENLKESCEKLGLVLLDHLIVGNKDYYSFREESEL 225
Cdd:PRK00024 161 ALKLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 13-222 1.40e-91

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: 268.08  E-value: 1.40e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  13 PRERLVEVGAERLSNQELLAIFIRTGTKKEPVSILSNKLLNRLESLAALRELSIEELQSLTGIGRVKAIEIKAMIELGKR 92
Cdd:COG2003   12 PRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAALELGRR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  93 INQSELLLNERILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMATSIII 172
Cdd:COG2003   92 LLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIIL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 636879336 173 VHNHPSGSVQPSRNDLLFTENLKESCEKLGLVLLDHLIVGNKDYYSFREE 222
Cdd:COG2003  172 AHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEE 221
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 13-225 3.76e-72

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: 218.85  E-value: 3.76e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336   13 PRERLVEVGAERLSNQELLAIFIRTGTKK-EPVSILSNKLLN---RLESLAALRELSIEELQSLTGIGRVKAIEIKAMIE 88
Cdd:TIGR00608   2 PREKLLKFGAEALSDYELLAIILRTGTPKgLDVLSLSKRLLDvfgRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336   89 LGKRINQSELLLNERILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMAT 168
Cdd:TIGR00608  82 LAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSAS 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 636879336  169 SIIIVHNHPSGSVQPSRNDLLFTENLKESCEKLGLVLLDHLIVGNKDYYSFREESEL 225
Cdd:TIGR00608 162 ALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 108-220 2.43e-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: 162.16  E-value: 2.43e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336 108 EKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMATSIIIVHNHPSGSVQPSRND 187
Cdd:cd08071    1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 636879336 188 LLFTENLKESCEKLGLVLLDHLIVGNKDYYSFR 220
Cdd:cd08071   81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 104-216 4.26e-47

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: 151.02  E-value: 4.26e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  104 ILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMATSIIIVHNHPSGSVQP 183
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 636879336  184 SRNDLLFTENLKESCEKLGLVLLDHLIVGNKDY 216
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
 
Name Accession Description Interval E-value
PRK00024 PRK00024
DNA repair protein RadC;
2-225 7.88e-107

DNA repair protein RadC;


Pssm-ID: 178801 [Multi-domain]  Cd Length: 224  Bit Score: 306.62  E-value: 7.88e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336   2 YQIEFKEEATLPRERLVEVGAERLSNQELLAIFIRTGTKKEPVSILSNKLLNRLESLAALRELSIEELQSLTGIGRVKAI 81
Cdd:PRK00024   1 MRIKDWPEEERPRERLLKYGAAALSDAELLAILLRTGTKGKSVLDLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  82 EIKAMIELGKRINQSELLLNERILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHY 161
Cdd:PRK00024  81 QLKAALELARRILAERLREREVLLSPEDVADYLMAELRDEEQEHFVVLFLDTKNRVIADEELFIGTLNSSIVHPREIVKR 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 636879336 162 AVKCMATSIIIVHNHPSGSVQPSRNDLLFTENLKESCEKLGLVLLDHLIVGNKDYYSFREESEL 225
Cdd:PRK00024 161 ALKLNAAALILAHNHPSGDPEPSQADILITKRLKEAGELLGIRLLDHIIIGDGEYVSFAERGLL 224
RadC COG2003
DNA repair protein RadC, contains a helix-hairpin-helix DNA-binding motif [Replication, ...
 13-222 1.40e-91

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: 268.08  E-value: 1.40e-91
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  13 PRERLVEVGAERLSNQELLAIFIRTGTKKEPVSILSNKLLNRLESLAALRELSIEELQSLTGIGRVKAIEIKAMIELGKR 92
Cdd:COG2003   12 PRERLLAKGAAALSDAELLAILLRTGTPGKDAVELAKELLARFGSLRGLLRASVEELRKIKGIGEAKAAQLKAALELGRR 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  93 INQSELLLNERILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMATSIII 172
Cdd:COG2003   92 LLREELEERPVISSPEDVADYLRARLAHLPREVFRVLFLDTKNRLIADEELSIGTLNHTPVYPREVFKRALRLNAAAIIL 171

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 636879336 173 VHNHPSGSVQPSRNDLLFTENLKESCEKLGLVLLDHLIVGNKDYYSFREE 222
Cdd:COG2003  172 AHNHPSGDPEPSRADIELTRRLKEAGELLGIRLLDHIIIGDGGYVSFAEE 221
radc TIGR00608
DNA repair protein radc; The genes in this family for which the functions are known have an as ...
 13-225 3.76e-72

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: 218.85  E-value: 3.76e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336   13 PRERLVEVGAERLSNQELLAIFIRTGTKK-EPVSILSNKLLN---RLESLAALRELSIEELQSLTGIGRVKAIEIKAMIE 88
Cdd:TIGR00608   2 PREKLLKFGAEALSDYELLAIILRTGTPKgLDVLSLSKRLLDvfgRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKAAVE 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336   89 LGKRINQSELLLNERILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMAT 168
Cdd:TIGR00608  82 LAKRYAKSRMLERPVIRSPEAAAEFLHTDLAHETREHFMVLFLDRKNRLIAKEVVFIGTVNHVPVHPREIFKEALKLSAS 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 636879336  169 SIIIVHNHPSGSVQPSRNDLLFTENLKESCEKLGLVLLDHLIVGNKDYYSFREESEL 225
Cdd:TIGR00608 162 ALILAHNHPSGEPSPSQEDILITERLRKAAELLGIELLDHLIIGKGRYVSFREEGLL 218
MPN_DUF2466 cd08071
Mov34/MPN/PAD-1 family; Mov34 DUF2466 (also known as DNA repair protein RadC) domain of ...
 108-220 2.43e-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: 162.16  E-value: 2.43e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336 108 EKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMATSIIIVHNHPSGSVQPSRND 187
Cdd:cd08071    1 EDVAEYLREELGDLDQEEFVVLLLDTKNRLIAVETISVGTLNSSLVHPREIFKEALRHNAAAIILAHNHPSGDPTPSRED 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 636879336 188 LLFTENLKESCEKLGLVLLDHLIVGNKDYYSFR 220
Cdd:cd08071   81 IELTKRLKEAGELLGIRLLDHIIVGDGGYFSFR 113
RadC pfam04002
RadC-like JAB domain; A family of proteins present widely across the bacteria. This family was ...
 104-216 4.26e-47

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: 151.02  E-value: 4.26e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336  104 ILGSEKLGRKMIHEIGHKKQEHLVALYLNTQNQIISQKTIFIGSVNRSIAEPREILHYAVKCMATSIIIVHNHPSGSVQP 183
Cdd:pfam04002   1 ITSPEDVAEYLMEELRDLDQEVFRVLFLDTKNRLIADEELSEGTLNSTLVHPREIFKRALRLNAAAVILAHNHPSGDPEP 80

                          90       100       110
                  ....*....|....*....|....*....|...
gi 636879336  184 SRNDLLFTENLKESCEKLGLVLLDHLIVGNKDY 216
Cdd:pfam04002  81 SREDIELTRRLKEAGELLGIRLLDHIIIGDGGY 113
UPF0758_N pfam20582
UPF0758 N-terminal; This domain is functionally uncharacterized, found at the N-terminal of ...
 13-75 5.19e-19

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: 77.70  E-value: 5.19e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 636879336   13 PRERLVEVGAERLSNQELLAIFIRTGTKKEPVSILSNKLLnRLESLAALRELSIEELQSLTGI 75
Cdd:pfam20582  10 PREKLLRYGAEALSDAELLAILLGSGTKGESAVDLARRLL-HFGGLRGLLKASVEELMKIKGI 71
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
 124-220 2.15e-08

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: 50.25  E-value: 2.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 636879336 124 EHLVALYLNTQNQIISQKTIFIGSvnrsiAEPREILHYAVKCM-ATSIIIVHNHPSGSVQPSRNDL-LFTenlkescekl 201
Cdd:cd08059   17 EFCGFLSGSKDNVMDELIFLPFVS-----GSVSAVIDLAALEIgMKVVGLVHSHPSGSCRPSEADLsLFT---------- 81

                         90
                 ....*....|....*....
gi 636879336 202 gLVLLDHLIVGNKDYYSFR 220
Cdd:cd08059   82 -RFGLYHVIVCYPYENSWK 99
MPN_archaeal cd08072
Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme; This family contains only ...
 168-212 9.29e-04

Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme; This family contains only archaeal 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.


Pssm-ID: 163703  Cd Length: 117  Bit Score: 38.01  E-value: 9.29e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 636879336 168 TSII-IVHNHPSGSVQPSRNDL-LFTenlkesceKLGLVlldHLIVG 212
Cdd:cd08072   59 MSIVgSVHSHPSGSPRPSDADLsFFS--------KTGLV---HIIVG 94
UvrC COG0322
Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];
50-85 1.48e-03

Excinuclease UvrABC, nuclease subunit [Replication, recombination and repair];


Pssm-ID: 440091 [Multi-domain]  Cd Length: 603  Bit Score: 39.34  E-value: 1.48e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 636879336  50 KLLNRLESLAALRELSIEELQSLTGIGRVKAIEIKA 85
Cdd:COG0322  563 ALLKHFGSLKAIKEASVEELAAVPGISKKLAEAIYE 598
uvrC PRK00558
excinuclease ABC subunit UvrC;
50-85 2.76e-03

excinuclease ABC subunit UvrC;


Pssm-ID: 234792 [Multi-domain]  Cd Length: 598  Bit Score: 38.18  E-value: 2.76e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 636879336  50 KLLNRLESLAALRELSIEELQSLTGIGRVKAIEIKA 85
Cdd:PRK00558 558 ALLKHFGSLKAIKEASVEELAKVPGISKKLAEAIYE 593
 
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.
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