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 500929387  2 KIITVKLPEQFLEAMDELVNTGRYETRSEVIRAAIGDFIRKELW 45
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 500929387  2 KIITVKLPEQFLEAMDELVNTGRYETRSEVIRAAIGDFIRKELW 45
Cdd:cd22231   1 ERISVSLPEELLEELDELVKEGGYSSRSEAIRDAIRELLEEEEE 44

nickel responsive regulator; Provisional

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 500929387   1 MKIITVKLPEQFLEAMDELVNTGRYETRSEVIRAAIGDFIRKELWIKD 48
Cdd:PRK01002   4 MMRISISLPDKLLGEFDEIIEERGYASRSEGIRDAIRDYIIKYKWMNS 51

Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH; ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, pfam05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins.

                         10        20        30
                 ....*....|....*....|....*....|..
gi 500929387   5 TVKLPEQFLEAMDELVNTGRYETRSEVIRAAI 36
Cdd:pfam03693  6 SVVLGEHFTAFIDSQIQGGRYGSASEVIRSAL 37

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 500929387  2 KIITVKLPEQFLEAMDELVNTGRYETRSEVIRAAIGDFIRKELW 45
Cdd:cd22231   1 ERISVSLPEELLEELDELVKEGGYSSRSEAIRDAIRELLEEEEE 44

Transcriptional regulator, contains Arc/MetJ-type RHH (ribbon-helix-helix) DNA-binding domain [Transcription];

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 500929387  2 KIITVKLPEQFLEAMDELVNTGRYETRSEVIRAAIGDFIRKELWIKD 48
Cdd:COG3609   1 ETMSISLPDELEDFIDEQVESGRYASASEVIREALRLLEEREAKLEA 47

nickel-responsive transcriptional regulator NikR;

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 500929387   6 VKLPEQFLEAMDELVNTGRYETRSEVIRAAIGDFIRKELW 45
Cdd:PRK04460   7 VSLDSDLLEKFDELIEEKGYQNRSEAIRDLIRDFLVEHEW 46

putative addiction module antidote protein, CC2985 family; This bacterial protein family has a very similar seed alignment to that of pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15. [Cellular processes, Other, Mobile and extrachromosomal element functions, Plasmid functions]

                         10        20        30
                 ....*....|....*....|....*....|....
gi 500929387   3 IITVKLPEQFLEAMDELVNTGRYETRSEVIRAAI 36
Cdd:TIGR02606  1 MTSVSLGEHLESFIRSQVQSGRYGSASEVIRAAL 34

Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH; ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, pfam05016. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria. Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerizes with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins.

                         10        20        30
                 ....*....|....*....|....*....|..
gi 500929387   5 TVKLPEQFLEAMDELVNTGRYETRSEVIRAAI 36
Cdd:pfam03693  6 SVVLGEHFTAFIDSQIQGGRYGSASEVIRSAL 37