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Conserved domains on  [gi|447041448|ref|WP_001118704|]
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MULTISPECIES: CopG family ribbon-helix-helix protein [Gammaproteobacteria]

Protein Classification

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NikR COG0864
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ...
 6-135 2.41e-32

Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain [Transcription];


:

Pssm-ID: 440624  Cd Length: 132  Bit Score: 111.13  E-value: 2.41e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   6 LARISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQAQA-NEVMVGTLTLLYDASQMTLRNQLVDLQQQFLA 84
Cdd:COG0864    1 MKRISVSLPDDLLEELDELVEEEGYSNRSEAIRDAIREYLAERKWREgDGEVVGVLTIVYDHHKRELSERLTDIQHEYRD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 447041448  85 QVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHLELMDA 135
Cdd:COG0864   81 LIISSLHVHLDHDNCLEVIVVRGEAEEIRELADKLRGLKGVKHGKLVLLPA 131
 
Name Accession Description Interval E-value
NikR COG0864
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ...
 6-135 2.41e-32

Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain [Transcription];


Pssm-ID: 440624  Cd Length: 132  Bit Score: 111.13  E-value: 2.41e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   6 LARISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQAQA-NEVMVGTLTLLYDASQMTLRNQLVDLQQQFLA 84
Cdd:COG0864    1 MKRISVSLPDDLLEELDELVEEEGYSNRSEAIRDAIREYLAERKWREgDGEVVGVLTIVYDHHKRELSERLTDIQHEYRD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 447041448  85 QVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHLELMDA 135
Cdd:COG0864   81 LIISSLHVHLDHDNCLEVIVVRGEAEEIRELADKLRGLKGVKHGKLVLLPA 131
PRK04460 PRK04460
nickel-responsive transcriptional regulator NikR;
5-130 3.13e-27

nickel-responsive transcriptional regulator NikR;


Pssm-ID: 179855  Cd Length: 137  Bit Score: 98.52  E-value: 3.13e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   5 KLARISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQAQA-NEVMVGTLTLLYDASQMTLRNQLVDLQQQFL 83
Cdd:PRK04460   1 ETIRFGVSLDSDLLEKFDELIEEKGYQNRSEAIRDLIRDFLVEHEWEEgDEEVAGTVTLVYNHHVSDLAQKLTEIQHDHH 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 447041448  84 AQVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHL 130
Cdd:PRK04460  81 DEIISSLHVHLDHHNCLEVLVLKGKAKEIKKIADRLISTKGVKHGKL 127
NikR_C pfam08753
NikR C terminal nickel binding domain; NikR is a transcription factor that regulates nickel ...
 58-130 6.09e-17

NikR C terminal nickel binding domain; NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains four nickel binding sites at the tetramer interface.


Pssm-ID: 462589  Cd Length: 75  Bit Score: 70.20  E-value: 6.09e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447041448   58 GTLTLLYDASQMTLRNQLVDLQQQFLAQVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHL 130
Cdd:pfam08753   1 GTITVVYDHHQRDLSERLTDIQHEYHDLIISTLHVHLDHDNCLEVIVLKGPAEEIRELADKLRALKGVKHGKL 73
RHH_NikR_HicB-like cd22231
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ...
 8-49 1.40e-07

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: 45.12  E-value: 1.40e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 447041448   8 RISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQ 49
Cdd:cd22231    2 RISVSLPEELLEELDELVKEGGYSSRSEAIRDAIRELLEEEE 43
 
Name Accession Description Interval E-value
NikR COG0864
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ...
 6-135 2.41e-32

Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain [Transcription];


Pssm-ID: 440624  Cd Length: 132  Bit Score: 111.13  E-value: 2.41e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   6 LARISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQAQA-NEVMVGTLTLLYDASQMTLRNQLVDLQQQFLA 84
Cdd:COG0864    1 MKRISVSLPDDLLEELDELVEEEGYSNRSEAIRDAIREYLAERKWREgDGEVVGVLTIVYDHHKRELSERLTDIQHEYRD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 447041448  85 QVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHLELMDA 135
Cdd:COG0864   81 LIISSLHVHLDHDNCLEVIVVRGEAEEIRELADKLRGLKGVKHGKLVLLPA 131
PRK04460 PRK04460
nickel-responsive transcriptional regulator NikR;
5-130 3.13e-27

nickel-responsive transcriptional regulator NikR;


Pssm-ID: 179855  Cd Length: 137  Bit Score: 98.52  E-value: 3.13e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   5 KLARISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQAQA-NEVMVGTLTLLYDASQMTLRNQLVDLQQQFL 83
Cdd:PRK04460   1 ETIRFGVSLDSDLLEKFDELIEEKGYQNRSEAIRDLIRDFLVEHEWEEgDEEVAGTVTLVYNHHVSDLAQKLTEIQHDHH 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 447041448  84 AQVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHL 130
Cdd:PRK04460  81 DEIISSLHVHLDHHNCLEVLVLKGKAKEIKKIADRLISTKGVKHGKL 127
PRK01002 PRK01002
nickel responsive regulator; Provisional
 4-125 5.00e-20

nickel responsive regulator; Provisional


Pssm-ID: 179203 [Multi-domain]  Cd Length: 141  Bit Score: 80.10  E-value: 5.00e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   4 QKLARISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQaQANEV---MVGTLTLLYDASQMTLRNQLVDLQQ 80
Cdd:PRK01002   2 TEMMRISISLPDKLLGEFDEIIEERGYASRSEGIRDAIRDYIIKYK-WMNSMegeRVGTISVIYDHHSTGVMEKLTDIQH 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 447041448  81 QFLAQVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGV 125
Cdd:PRK01002  81 DYSDLIVASLHIHLDHDHCLEVIVVRGDAKEIRELTEKLMALKGV 125
PRK00630 PRK00630
nickel responsive regulator; Provisional
 3-125 9.55e-20

nickel responsive regulator; Provisional


Pssm-ID: 234805  Cd Length: 148  Bit Score: 79.45  E-value: 9.55e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   3 KQKLARISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLI----AEQAQANEVMVGTLTLLYDASQMTLRNQLVDL 78
Cdd:PRK00630   7 DDSIIRFSVSLQQNLLDELDNRIIKNGYSSRSELVRDLIREKLVednwAEDNPNDESKIAVLVVIYDHHQRELNQRMIDI 86

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 447041448  79 QQQFLAQVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGV 125
Cdd:PRK00630  87 QHASGTHILCTTHIHMDHHNCLETIILRGNSFEIQRLQLEIGGLKGV 133
NikR_C pfam08753
NikR C terminal nickel binding domain; NikR is a transcription factor that regulates nickel ...
 58-130 6.09e-17

NikR C terminal nickel binding domain; NikR is a transcription factor that regulates nickel uptake. It consists of two dimeric DNA binding domains separated by a tetrameric regulatory domain that binds nickel. This domain corresponds to the C terminal regulatory domain which contains four nickel binding sites at the tetramer interface.


Pssm-ID: 462589  Cd Length: 75  Bit Score: 70.20  E-value: 6.09e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447041448   58 GTLTLLYDASQMTLRNQLVDLQQQFLAQVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHL 130
Cdd:pfam08753   1 GTITVVYDHHQRDLSERLTDIQHEYHDLIISTLHVHLDHDNCLEVIVLKGPAEEIRELADKLRALKGVKHGKL 73
PRK02967 PRK02967
nickel-responsive transcriptional regulator NikR;
8-132 1.25e-13

nickel-responsive transcriptional regulator NikR;


Pssm-ID: 235093  Cd Length: 139  Bit Score: 63.50  E-value: 1.25e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 447041448   8 RISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLiaEQAQANEVM----VGTLTLLYDASQMTLRNQLVDLQQQFL 83
Cdd:PRK02967   3 RVTITLDDDLLETLDSLIARRGYQNRSEAIRDLLRAAL--AQERTQEHQgtqcVAVLSYVYDHEKRDLASRLVSTQHHHH 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 447041448  84 AQVISSLHIQLDQQKILQVMLMQGASSELRQISQQFIVLKGVIKGHLEL 132
Cdd:PRK02967  81 DLSVATLHVHLDHDDCLEVAVLKGDTGDVQHFADDVIAERGVRHGHLQC 129
RHH_NikR_HicB-like cd22231
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ...
 8-49 1.40e-07

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: 45.12  E-value: 1.40e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 447041448   8 RISITVPESTLNALDQKIVEQNYESRSQAIVDMINKHLIAEQ 49
Cdd:cd22231    2 RISVSLPEELLEELDELVKEGGYSSRSEAIRDAIRELLEEEE 43
 
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.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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