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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 818897933  6 TVLSVSLPPKLSKAVDKLSKQTS-QTRSELIRNALRDYILNFEE 48
Cdd:cd22231   1 ERISVSLPEELLEELDELVKEGGySSRSEAIRDAIRELLEEEEE 44

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 818897933  6 TVLSVSLPPKLSKAVDKLSKQTS-QTRSELIRNALRDYILNFEE 48
Cdd:cd22231   1 ERISVSLPEELLEELDELVKEGGySSRSEAIRDAIRELLEEEEE 44

nickel responsive regulator; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 818897933   8 LSVSLPPKLSKAVDK-LSKQTSQTRSELIRNALRDYILNFE 47
Cdd:PRK01002   7 ISISLPDKLLGEFDEiIEERGYASRSEGIRDAIRDYIIKYK 47

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 818897933  6 TVLSVSLPPKLSKAVDKLSKQTS-QTRSELIRNALRDYILNFEE 48
Cdd:cd22231   1 ERISVSLPEELLEELDELVKEGGySSRSEAIRDAIRELLEEEEE 44

nickel responsive regulator; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 818897933   8 LSVSLPPKLSKAVDK-LSKQTSQTRSELIRNALRDYILNFE 47
Cdd:PRK01002   7 ISISLPDKLLGEFDEiIEERGYASRSEGIRDAIRDYIIKYK 47

ribbon-helix-helix domain of Shewanella oneidensis type II antitoxin CopA(SO), and similar proteins; This family includes the N-terminal ribbon-helix-helix (RHH) domain of Shewanella oneidensis CopA(SO), a newly identified type II antitoxin, as well as the N-terminal RHH domain of Escherichia coli PutA flavoprotein, among other similar proteins, many of which are as yet uncharacterized. CopA(SO) is a typical RHH antitoxin that includes an ordered N-terminal domain (CopA(SO)-N) and a disordered C-terminal domain (CopA(SO)-C). Biophysical investigation indicates allosteric effects of CopA(SO)-N on CopA(SO)-C; DNA binding of CopA(SO)-N appears to induce CopA(SO)-C to fold and self-associate the C-terminal domain. The multifunctional E. coli proline utilization A (PutA) flavoprotein functions as a membrane-associated proline catabolic enzyme as well as a transcriptional repressor of the proline utilization genes putA and putP. The N-terminal domain of PutA is a transcriptional regulator with an RHH fold; structure studies show that it forms a homodimer to bind one DNA duplex. This family also includes orphan antitoxin ParD2, an antitoxin component of a non-functional type II toxin-antitoxin (TA system); it does not neutralize the effect of any of the RelE or ParE toxins.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 818897933  6 TVLSVSLPPKLSKAVDKLSKQTSQTRSELIRNALRDYILNFEE 48
Cdd:cd22233   1 TTLSVRLDDDLKERLDRLAAATDRSRSWIIKEAIEEYLEREEW 43

Family of unknown function (DUF6290); This family of proteins is functionally uncharacterized, they are predominantly found in bacteria but also in viruses. Proteins in this family are approximately 80 amino acids in length and presumably contain a ribbon-helix-helix DNA-binding motif.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 818897933   6 TVLSVSLPPKLSKAVDKLSKQTSQTRSELIRNALRDYIlnfEEDITLS---KLAELRDTNNAKYLSHKEVW 73
Cdd:pfam19807  2 STISVRLNEEEEELIKKYAKLKGISLSELIRQALLEKI---EDEYDLKiyeEYAAEKKKGDPKTYSHDEVK 69

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.

                        10        20        30
                ....*....|....*....|....*....|....*
gi 818897933  8 LSVSLPPKLSKAVDKLSKQTSQTRSELIRNALRDY 42
Cdd:cd21631   3 VTIKLDDELLERLDELARKRGVSRSELIREALREY 37

ribbon-helix-helix domain containing protein

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 818897933  7 VLSVSLPPKLSKAVDKLSKQTSQTRSELIRNALRDYILN 45
Cdd:PHA00617 41 VISFKLPPELNAKLEQVAIKMKKSKSEIIREALEKYLEE 79