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MULTISPECIES: CopG family ribbon-helix-helix protein [Brevibacillus]
CopG family ribbon-helix-helix protein( domain architecture ID 11436749)
CopG family ribbon-helix-helix (RHH) protein similar to CopG/NikR family transcriptional regulators and to Bacillus subtilis antitoxin EndoAI (MazE), which inactivates the toxin EndoA (MazF), an mRNA interferase that cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest
List of domain hits
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Name | Accession | Description | Interval | E-value | |||
NikR | COG0864 | Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ... |
13-99 | 1.54e-15 | |||
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain [Transcription]; : Pssm-ID: 440624 Cd Length: 132 Bit Score: 66.45 E-value: 1.54e-15
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Name | Accession | Description | Interval | E-value | |||
NikR | COG0864 | Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ... |
13-99 | 1.54e-15 | |||
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain [Transcription]; Pssm-ID: 440624 Cd Length: 132 Bit Score: 66.45 E-value: 1.54e-15
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RHH_NikR_HicB-like | cd22231 | ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ... |
14-56 | 6.75e-10 | |||
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ParD, and MazE, and similar proteins; This family includes the N-terminal domain of NikR, C-terminal domains of antitoxins HicB and ParD, as well as antitoxin MazE, and similar proteins, all of which belong to the ribbon-helix-helix (RHH) family of transcription factors. NikR is a nickel-responsive transcription factor that consists of an N-terminal DNA-binding RHH domain and a C-terminal metal-binding domain (MBD) with four nickel ions. In Helicobacter pylori, which colonizes the gastric epithelium of humans leading to gastric ulcers and gastric cancers, NikR (HpNikR) regulates multiple genes. It regulates urease, which protects H. pylori from acidic shock at low pH, by converting urea to ammonia and bicarbonate. It also plays a complex role in the intracellular physiology of nickel; occupation of nickel-binding sites results in NikR binding to its operator in the nickel permease nikABCDE promoter. Thus, there is weaker repression of NikABCDE transcription at low intracellular free nickel concentrations while strong repression prevails at higher concentrations, which would be potentially toxic. Antitoxin HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In the pathogen Burkholderia pseudomallei, the HicAB system plays a role in regulating the frequency of persister cells and may therefore play a role in disease. Structural studies of Yersinia pestis HicB show that it acts as an autoregulatory protein and HicA acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. Similarly, Caulobacter crescentus ParD antitoxin neutralizes the effect of cognate ParE toxin. In Bacillus subtilis, during stress conditions, antitoxin MazE binds to toxin MazF, an mRNA interferase, and inactivates it and cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest. Pssm-ID: 409021 [Multi-domain] Cd Length: 44 Bit Score: 49.74 E-value: 6.75e-10
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RHH_1 | pfam01402 | Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the ... |
15-53 | 1.66e-03 | |||
Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected. Pssm-ID: 426244 Cd Length: 39 Bit Score: 33.25 E-value: 1.66e-03
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Name | Accession | Description | Interval | E-value | |||
NikR | COG0864 | Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ... |
13-99 | 1.54e-15 | |||
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain [Transcription]; Pssm-ID: 440624 Cd Length: 132 Bit Score: 66.45 E-value: 1.54e-15
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RHH_NikR_HicB-like | cd22231 | ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ... |
14-56 | 6.75e-10 | |||
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ParD, and MazE, and similar proteins; This family includes the N-terminal domain of NikR, C-terminal domains of antitoxins HicB and ParD, as well as antitoxin MazE, and similar proteins, all of which belong to the ribbon-helix-helix (RHH) family of transcription factors. NikR is a nickel-responsive transcription factor that consists of an N-terminal DNA-binding RHH domain and a C-terminal metal-binding domain (MBD) with four nickel ions. In Helicobacter pylori, which colonizes the gastric epithelium of humans leading to gastric ulcers and gastric cancers, NikR (HpNikR) regulates multiple genes. It regulates urease, which protects H. pylori from acidic shock at low pH, by converting urea to ammonia and bicarbonate. It also plays a complex role in the intracellular physiology of nickel; occupation of nickel-binding sites results in NikR binding to its operator in the nickel permease nikABCDE promoter. Thus, there is weaker repression of NikABCDE transcription at low intracellular free nickel concentrations while strong repression prevails at higher concentrations, which would be potentially toxic. Antitoxin HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In the pathogen Burkholderia pseudomallei, the HicAB system plays a role in regulating the frequency of persister cells and may therefore play a role in disease. Structural studies of Yersinia pestis HicB show that it acts as an autoregulatory protein and HicA acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. Similarly, Caulobacter crescentus ParD antitoxin neutralizes the effect of cognate ParE toxin. In Bacillus subtilis, during stress conditions, antitoxin MazE binds to toxin MazF, an mRNA interferase, and inactivates it and cleaves mRNAs in a sequence-specific manner, resulting in cellular growth arrest. Pssm-ID: 409021 [Multi-domain] Cd Length: 44 Bit Score: 49.74 E-value: 6.75e-10
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ParD | COG3609 | Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain ... |
14-67 | 2.59e-05 | |||
Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain [Transcription]; Pssm-ID: 442827 Cd Length: 77 Bit Score: 39.03 E-value: 2.59e-05
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RHH_1 | pfam01402 | Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the ... |
15-53 | 1.66e-03 | |||
Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerization and not DNA binding as might have been expected. Pssm-ID: 426244 Cd Length: 39 Bit Score: 33.25 E-value: 1.66e-03
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HicB_lk_antitox | pfam15919 | HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like ... |
13-46 | 4.59e-03 | |||
HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like antitoxins. Pssm-ID: 435020 [Multi-domain] Cd Length: 123 Bit Score: 33.78 E-value: 4.59e-03
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RHH_CopG_NikR-like | cd21631 | ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription ... |
14-53 | 7.05e-03 | |||
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription factor NikR, and similar proteins; This family includes the ribbon-helix-helix (RHH) domains of transcriptional repressor CopG, nickel-responsive transcription factor NikR, several antitoxins such as Shewanella oneidensis CopA(SO), Burkholderia pseudomallei HicB, and Caulobacter crescentus ParD, and similar proteins. CopG, a homodimeric RHH protein of around 45 residues, constitutes one of the smallest natural transcriptional repressors characterized and is the prototype of a series of repressor proteins encoded by plasmids that exhibit a similar genetic structure at their leading strand initiation and control regions. It is involved in the control of plasmid copy number. NikR, which consists of the N-terminal DNA-binding RHH domain and the C-terminal metal-binding domain (MBD) with four nickel ions, regulates several genes; in Helicobacter pylori, NikR regulates the urease enzyme under extreme acidic conditions, and is involved in the intracellular physiology of nickel. Protein HicB is part of the HicAB toxin-antitoxin (TA) system, where the toxins are RNases, found in many bacteria. In Burkholderia pseudomallei, the HicAB system may play a role in disease by regulating the frequency of persister cells, while in Yersinia pestis HicB acts as an autoregulatory protein that inhibits HicA, which acts as an mRNase. In Escherichia coli, an excess of HicA has been shown to de-repress a HicB-DNA complex and restore transcription of HicB. The CopG family RHH domain, represented by this model, forms a homodimer and binds DNA. Pssm-ID: 409020 Cd Length: 42 Bit Score: 31.71 E-value: 7.05e-03
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