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Conserved domains on  [gi|1623367058|gb|THO04107|]
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ribbon-helix-helix domain-containing protein [Klebsiella pneumoniae subsp. pneumoniae]

Protein Classification

CopG family transcriptional regulator( domain architecture ID 15348592)

CopG family transcriptional regulator is a ribbon-helix-helix (RHH) protein similar to Mycobacterium VapB antitoxins and Streptococcus agalactiae protein CopG, which regulates plasmid copy number by binding to the RepAB promoter

Gene Ontology:  GO:0006276|GO:0006355|GO:0032993

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RHH_CopG_NikR-like cd21631
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription ...
 11-51 1.24e-04

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: 35.95  E-value: 1.24e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1623367058 11 RILLDLSDDVIQRLDDLKVQRNIPRAELLREAVEQYLEKQD 51
Cdd:cd21631    2 RVTIKLDDELLERLDELARKRGVSRSELIREALREYLERLE 42
 
Name Accession Description Interval E-value
RHH_CopG_NikR-like cd21631
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription ...
 11-51 1.24e-04

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: 35.95  E-value: 1.24e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1623367058 11 RILLDLSDDVIQRLDDLKVQRNIPRAELLREAVEQYLEKQD 51
Cdd:cd21631    2 RVTIKLDDELLERLDELARKRGVSRSELIREALREYLERLE 42
RHH_3 pfam12651
Ribbon-helix-helix domain; This short bacterial protein contains a ribbon-helix-helix domain ...
 11-49 1.85e-03

Ribbon-helix-helix domain; This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding.


Pssm-ID: 289422  Cd Length: 44  Bit Score: 33.03  E-value: 1.85e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1623367058 11 RILLDLSDDVIQRLDDLKVQRNIPRAELLREAVEQYLEK 49
Cdd:pfam12651  4 RTTVSIDPELAEKLKALSEKTRIPRSKLLDEAIELLLEK 42
PRK11675 PRK11675
LexA regulated protein; Provisional
 11-49 5.21e-03

LexA regulated protein; Provisional


Pssm-ID: 183272  Cd Length: 90  Bit Score: 32.64  E-value: 5.21e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1623367058 11 RILLDLSDDVIQRLDDLKVQRNIPRAELLREAVEQYLEK 49
Cdd:PRK11675  52 RVELKLNADLVDALNELAEARNISRSELIEEILMKQLAA 90
 
Name Accession Description Interval E-value
RHH_CopG_NikR-like cd21631
ribbon-helix-helix domains of transcription repressor CopG, nickel responsive transcription ...
 11-51 1.24e-04

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: 35.95  E-value: 1.24e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1623367058 11 RILLDLSDDVIQRLDDLKVQRNIPRAELLREAVEQYLEKQD 51
Cdd:cd21631    2 RVTIKLDDELLERLDELARKRGVSRSELIREALREYLERLE 42
RHH_3 pfam12651
Ribbon-helix-helix domain; This short bacterial protein contains a ribbon-helix-helix domain ...
 11-49 1.85e-03

Ribbon-helix-helix domain; This short bacterial protein contains a ribbon-helix-helix domain that is likely to be DNA-binding.


Pssm-ID: 289422  Cd Length: 44  Bit Score: 33.03  E-value: 1.85e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1623367058 11 RILLDLSDDVIQRLDDLKVQRNIPRAELLREAVEQYLEK 49
Cdd:pfam12651  4 RTTVSIDPELAEKLKALSEKTRIPRSKLLDEAIELLLEK 42
PRK11675 PRK11675
LexA regulated protein; Provisional
 11-49 5.21e-03

LexA regulated protein; Provisional


Pssm-ID: 183272  Cd Length: 90  Bit Score: 32.64  E-value: 5.21e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 1623367058 11 RILLDLSDDVIQRLDDLKVQRNIPRAELLREAVEQYLEK 49
Cdd:PRK11675  52 RVELKLNADLVDALNELAEARNISRSELIEEILMKQLAA 90
 
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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