NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446421888|ref|WP_000499743|]
View 

type II toxin-antitoxin system HicB family antitoxin [Escherichia coli]

Protein Classification

type II toxin-antitoxin system HicB family antitoxin( domain architecture ID 581201)

type II toxin-antitoxin system HicB family antitoxin is the antitoxin component of a type II toxin-antitoxin (TA) system and functions as an mRNA interferase antitoxin preventing effects of the cognate HicA family toxin

Gene Ontology:  GO:0110001
PubMed:  30337369|16895922|28279904
SCOP:  4001747

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HicB_lk_antitox super family cl23837
HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like ...
 3-129 9.10e-47

HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like antitoxins.


The actual alignment was detected with superfamily member pfam15919:

Pssm-ID: 451570 [Multi-domain]  Cd Length: 123  Bit Score: 147.41  E-value: 9.10e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446421888    3 YPAYIHSDpDGSASGF-FPDVPGCYFAGDTLDNAFQDARSALVAHFETLCEMNEELPLPGSVETHLVQraQDFIGGQWLL 81
Cdd:pfam15919   1 YPIAIEKD-EDSAYGVvVPDLPGCFSAGDTLEEAIANAEEAIELHIEGLIEDGEAIPAPSSIEELQAN--PEYAGWIWAL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 446421888   82 VDINMNQFEGRAERINITMPKRLLNKIDTYVRNNPDyaNRSAFLAEAA 129
Cdd:pfam15919  78 VDIDLSPLDGKSERINITLPRRVLRRIDAYAKAAGE--TRSGFLARAA 123
 
Name Accession Description Interval E-value
HicB_lk_antitox pfam15919
HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like ...
 3-129 9.10e-47

HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like antitoxins.


Pssm-ID: 435020 [Multi-domain]  Cd Length: 123  Bit Score: 147.41  E-value: 9.10e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446421888    3 YPAYIHSDpDGSASGF-FPDVPGCYFAGDTLDNAFQDARSALVAHFETLCEMNEELPLPGSVETHLVQraQDFIGGQWLL 81
Cdd:pfam15919   1 YPIAIEKD-EDSAYGVvVPDLPGCFSAGDTLEEAIANAEEAIELHIEGLIEDGEAIPAPSSIEELQAN--PEYAGWIWAL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 446421888   82 VDINMNQFEGRAERINITMPKRLLNKIDTYVRNNPDyaNRSAFLAEAA 129
Cdd:pfam15919  78 VDIDLSPLDGKSERINITLPRRVLRRIDAYAKAAGE--TRSGFLARAA 123
HicB COG1598
Antitoxin component HicB of the HicAB toxin-antitoxin system [Defense mechanisms];
3-66 7.99e-20

Antitoxin component HicB of the HicAB toxin-antitoxin system [Defense mechanisms];


Pssm-ID: 441206  Cd Length: 65  Bit Score: 76.85  E-value: 7.99e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446421888   3 YPAYIHSDPDGSASGFFPDVPGCYFAGDTLDNAFQDARSALVAHFETLCEMNEELPLPGSVETH 66
Cdd:COG1598    2 YPAIIEKDEDGGYVAEVPDLPGCVTQGDTLEEALENAKEALELHLEALLEDGEPIPEPSSIEET 65
RHH_NikR_HicB-like cd22231
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ...
 94-133 4.62e-09

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: 48.97  E-value: 4.62e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446421888  94 ERINITMPKRLLNKIDTYVRNNpDYANRSAFLAEAARRVL 133
Cdd:cd22231    1 ERISVSLPEELLEELDELVKEG-GYSSRSEAIRDAIRELL 39
 
Name Accession Description Interval E-value
HicB_lk_antitox pfam15919
HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like ...
 3-129 9.10e-47

HicB_like antitoxin of bacterial toxin-antitoxin system; This is a family of HicB-like antitoxins.


Pssm-ID: 435020 [Multi-domain]  Cd Length: 123  Bit Score: 147.41  E-value: 9.10e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446421888    3 YPAYIHSDpDGSASGF-FPDVPGCYFAGDTLDNAFQDARSALVAHFETLCEMNEELPLPGSVETHLVQraQDFIGGQWLL 81
Cdd:pfam15919   1 YPIAIEKD-EDSAYGVvVPDLPGCFSAGDTLEEAIANAEEAIELHIEGLIEDGEAIPAPSSIEELQAN--PEYAGWIWAL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 446421888   82 VDINMNQFEGRAERINITMPKRLLNKIDTYVRNNPDyaNRSAFLAEAA 129
Cdd:pfam15919  78 VDIDLSPLDGKSERINITLPRRVLRRIDAYAKAAGE--TRSGFLARAA 123
HicB COG1598
Antitoxin component HicB of the HicAB toxin-antitoxin system [Defense mechanisms];
3-66 7.99e-20

Antitoxin component HicB of the HicAB toxin-antitoxin system [Defense mechanisms];


Pssm-ID: 441206  Cd Length: 65  Bit Score: 76.85  E-value: 7.99e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446421888   3 YPAYIHSDPDGSASGFFPDVPGCYFAGDTLDNAFQDARSALVAHFETLCEMNEELPLPGSVETH 66
Cdd:COG1598    2 YPAIIEKDEDGGYVAEVPDLPGCVTQGDTLEEALENAKEALELHLEALLEDGEPIPEPSSIEET 65
RHH_NikR_HicB-like cd22231
ribbon-helix-helix domains of nickel responsive transcription factor NikR, antitoxins HicB, ...
 94-133 4.62e-09

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: 48.97  E-value: 4.62e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446421888  94 ERINITMPKRLLNKIDTYVRNNpDYANRSAFLAEAARRVL 133
Cdd:cd22231    1 ERISVSLPEELLEELDELVKEG-GYSSRSEAIRDAIRELL 39
NikR COG0864
Metal-responsive transcriptional regulator, contains CopG/Arc/MetJ DNA-binding domain ...
 94-133 3.11e-05

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


Pssm-ID: 440624  Cd Length: 132  Bit Score: 40.64  E-value: 3.11e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446421888  94 ERINITMPKRLLNKIDTYVRNNpDYANRSAFLAEAARRVL 133
Cdd:COG0864    2 KRISVSLPDDLLEELDELVEEE-GYSNRSEAIRDAIREYL 40
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH