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Conserved domains on  [gi|445615040|gb|ELY68699|]
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CopG domain protein DNA-binding domain protein [Natrinema versiforme JCM 10478]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RHH_CopG_archaea cd22235
ribbon-helix-helix domain of CopG family transcriptional regulators found in archaea; This ...
 4-45 1.27e-16

ribbon-helix-helix domain of CopG family transcriptional regulators found in archaea; This subfamily includes the N-terminal ribbon-helix-helix (RHH) domain of putative transcriptional repressor CopG from archaea, and similar proteins. These uncharacterized proteins have a typical RHH, similar to plasmid-encoded transcriptional repressor CopG, the protein that is encoded by the promiscuous streptococcal plasmid pMV158 and is involved in the control of plasmid copy number.


:

Pssm-ID: 409025  Cd Length: 43  Bit Score: 69.73  E-value: 1.27e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 445615040   4 RVTVSLDDDSAAALETLVAETGNGQSEVVRRALTFYAANFEA 45
Cdd:cd22235    2 RITISLDEETKEILEELKKETGKSQSEIIRRALKFYYENRDL 43
 
Name Accession Description Interval E-value
RHH_CopG_archaea cd22235
ribbon-helix-helix domain of CopG family transcriptional regulators found in archaea; This ...
 4-45 1.27e-16

ribbon-helix-helix domain of CopG family transcriptional regulators found in archaea; This subfamily includes the N-terminal ribbon-helix-helix (RHH) domain of putative transcriptional repressor CopG from archaea, and similar proteins. These uncharacterized proteins have a typical RHH, similar to plasmid-encoded transcriptional repressor CopG, the protein that is encoded by the promiscuous streptococcal plasmid pMV158 and is involved in the control of plasmid copy number.


Pssm-ID: 409025  Cd Length: 43  Bit Score: 69.73  E-value: 1.27e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 445615040   4 RVTVSLDDDSAAALETLVAETGNGQSEVVRRALTFYAANFEA 45
Cdd:cd22235    2 RITISLDEETKEILEELKKETGKSQSEIIRRALKFYYENRDL 43
RHH_1 pfam01402
Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the ...
 4-41 7.38e-07

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: 44.04  E-value: 7.38e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 445615040    4 RVTVSLDDDSAAALETLVAETGNGQSEVVRRALTFYAA 41
Cdd:pfam01402   1 RVSISLDEELLERLDELARARGRSRSELIREALREYLE 38
PRK02967 PRK02967
nickel-responsive transcriptional regulator NikR;
3-33 4.05e-03

nickel-responsive transcriptional regulator NikR;


Pssm-ID: 235093  Cd Length: 139  Bit Score: 35.77  E-value: 4.05e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 445615040   3 QRVTVSLDDDSAAALETLVAETG-NGQSEVVR 33
Cdd:PRK02967   2 QRVTITLDDDLLETLDSLIARRGyQNRSEAIR 33
NikR COG0864
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ...
 2-36 8.72e-03

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


Pssm-ID: 440624  Cd Length: 132  Bit Score: 34.86  E-value: 8.72e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 445615040   2 TQRVTVSLDDDSAAALETLVAETG-NGQSEVVRRAL 36
Cdd:COG0864    1 MKRISVSLPDDLLEELDELVEEEGySNRSEAIRDAI 36
 
Name Accession Description Interval E-value
RHH_CopG_archaea cd22235
ribbon-helix-helix domain of CopG family transcriptional regulators found in archaea; This ...
 4-45 1.27e-16

ribbon-helix-helix domain of CopG family transcriptional regulators found in archaea; This subfamily includes the N-terminal ribbon-helix-helix (RHH) domain of putative transcriptional repressor CopG from archaea, and similar proteins. These uncharacterized proteins have a typical RHH, similar to plasmid-encoded transcriptional repressor CopG, the protein that is encoded by the promiscuous streptococcal plasmid pMV158 and is involved in the control of plasmid copy number.


Pssm-ID: 409025  Cd Length: 43  Bit Score: 69.73  E-value: 1.27e-16
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 445615040   4 RVTVSLDDDSAAALETLVAETGNGQSEVVRRALTFYAANFEA 45
Cdd:cd22235    2 RITISLDEETKEILEELKKETGKSQSEIIRRALKFYYENRDL 43
RHH_1 pfam01402
Ribbon-helix-helix protein, copG family; The structure of this protein repressor, which is the ...
 4-41 7.38e-07

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: 44.04  E-value: 7.38e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 445615040    4 RVTVSLDDDSAAALETLVAETGNGQSEVVRRALTFYAA 41
Cdd:pfam01402   1 RVSISLDEELLERLDELARARGRSRSELIREALREYLE 38
RHH_CopG_NikR-like cd21631
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription ...
 3-39 1.77e-05

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: 40.18  E-value: 1.77e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 445615040   3 QRVTVSLDDDSAAALETLVAETGNGQSEVVRRALTFY 39
Cdd:cd21631    1 KRVTIKLDDELLERLDELARKRGVSRSELIREALREY 37
PRK02967 PRK02967
nickel-responsive transcriptional regulator NikR;
3-33 4.05e-03

nickel-responsive transcriptional regulator NikR;


Pssm-ID: 235093  Cd Length: 139  Bit Score: 35.77  E-value: 4.05e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 445615040   3 QRVTVSLDDDSAAALETLVAETG-NGQSEVVR 33
Cdd:PRK02967   2 QRVTITLDDDLLETLDSLIARRGyQNRSEAIR 33
NikR COG0864
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ...
 2-36 8.72e-03

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


Pssm-ID: 440624  Cd Length: 132  Bit Score: 34.86  E-value: 8.72e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 445615040   2 TQRVTVSLDDDSAAALETLVAETG-NGQSEVVRRAL 36
Cdd:COG0864    1 MKRISVSLPDDLLEELDELVEEEGySNRSEAIRDAI 36
 
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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