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Protein

Antitoxin HipB

Gene

hipB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Antitoxin component of a type II toxin-antitoxin (TA) module. Neutralizes the toxic effect of cognate toxin HipA (PubMed:20616060). Also neutralizes the toxic effect of non-cognate toxin YjjJ (PubMed:28430938). Binds to operator sites with the consensus sequence 5-'TATCCN8GGATA-3' to repress the hipBA operon promoter (PubMed:8021189, PubMed:19150849); binding of HipB2 to DNA induces a 70 degree bend (PubMed:19150849). This forces HipA dimerization, which blocks HipA's active site and thus its toxic action (PubMed:26222023). May play a role in biofilm formation (PubMed:23329678).6 Publications

Enzyme regulationi

Degraded by Lon protease; degradation is inhibited in a HipA-HipB complex and when bound to the operator consensus sequence dsDNA.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi21 – 47H-T-H motifPROSITE-ProRule annotation1 PublicationAdd BLAST27

GO - Molecular functioni

  • bacterial-type RNA polymerase core promoter sequence-specific DNA binding Source: EcoCyc
  • bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding Source: CollecTF
  • sequence-specific DNA binding Source: EcoCyc
  • transcription regulatory region sequence-specific DNA binding Source: CollecTF

GO - Biological processi

  • negative regulation of transcription, DNA-templated Source: EcoCyc
  • transcription, DNA-templated Source: EcoCyc

Keywordsi

Molecular functionDNA-binding, Repressor
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyciEcoCyc:EG10442-MONOMER.
MetaCyc:EG10442-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Antitoxin HipB
Gene namesi
Name:hipB
Ordered Locus Names:b1508, JW1501
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10442. hipB.

Subcellular locationi

GO - Cellular componenti

  • protein-DNA complex Source: CollecTF

Pathology & Biotechi

Disruption phenotypei

Cannot be disrupted, suggesting it is a functional antitoxin; no visible phenotype when the hipBA operon is deleted (PubMed:8021189, PubMed:20616060). A hipA or a hipB-hipA operon deletion show decreased biofilm production in the absence of antibiotics (PubMed:23329678).3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi73 – 88Missing : Increased half-life in vivo and in vitro, no change in DNA or HipA-binding. 1 PublicationAdd BLAST16
Mutagenesisi88W → A: No change in DNA or HipA-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001497261 – 88Antitoxin HipBAdd BLAST88

Post-translational modificationi

Degraded by Lon protease in vivo; half-life is 17 minutes in wild-type cells and over 200 minutes in a lon deletion strain. In vitro degradation by Lon is Mg2+-ATP-dependent (PubMed:22720069).1 Publication

Proteomic databases

PaxDbiP23873.
PRIDEiP23873.

Expressioni

Gene expression databases

CollecTFiEXPREG_00000960.

Interactioni

Subunit structurei

Homodimer (PubMed:8021189). Binds operator DNA sites in the absence of HipA, inducing a 70 degree bend in consecutive operators and deforming DNA between the operators so that HipB dimers bind on opposite faces of the DNA (PubMed:26222023). Forms a HipA2HipB2 heterotetramer which can interact with a single operator site on DNA, inducing a 70 degree bend (PubMed:19150849). When 2 operators are present each HipB dimer contacts 1 HipA molecule, which are brought together by the DNA bend and dimerize, blocking the HipA active site and inactivating its toxic activity (PubMed:26222023). HipA-HipB-induced bending also distorts the -35 and -10 boxes of the promoter and probably prevents sigma-factor binding, and additionally bound HipB and HipA block RNA polymerase access to the -35 box, thus repressing the operon (PubMed:26222023). This complex also blocks the toxic activity of HipA (PubMed:19150849). Mutations present in allele hipA7 (G22S and D291A) decrease the affinity of HipA for HipB (PubMed:20616060).6 Publications

Protein-protein interaction databases

BioGridi4260221. 3 interactors.
DIPiDIP-9899N.
IntActiP23873. 2 interactors.
STRINGi316385.ECDH10B_1639.

Structurei

Secondary structure

188
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi10 – 23Combined sources14
Helixi28 – 35Combined sources8
Helixi39 – 47Combined sources9
Helixi49 – 51Combined sources3
Helixi54 – 63Combined sources10
Beta strandi66 – 72Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2WIUX-ray2.35B/D1-88[»]
3DNVX-ray2.68B1-88[»]
3HZIX-ray2.98B1-88[»]
4YG1X-ray3.25A/B/C/D1-72[»]
4YG4X-ray3.50A/B/C/D4-74[»]
4YG7X-ray3.77B/C/E/G4-74[»]
4Z58X-ray2.50A4-74[»]
4Z59X-ray2.30A4-74[»]
4Z5CX-ray2.50A/B4-74[»]
4Z5DX-ray2.15A/B4-74[»]
4Z5HX-ray2.10A3-74[»]
5K98X-ray3.99B/P1-88[»]
ProteinModelPortaliP23873.
SMRiP23873.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP23873.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini17 – 71HTH cro/C1-typePROSITE-ProRule annotation1 PublicationAdd BLAST55

Phylogenomic databases

eggNOGiENOG41061P8. Bacteria.
COG1396. LUCA.
HOGENOMiHOG000225389.
InParanoidiP23873.
KOiK15773.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiView protein in InterPro
IPR001387. Cro/C1-type_HTH.
IPR010982. Lambda_DNA-bd_dom.
IPR011991. WHTH_DNA-bd_dom.
PfamiView protein in Pfam
PF01381. HTH_3. 1 hit.
SMARTiView protein in SMART
SM00530. HTH_XRE. 1 hit.
SUPFAMiSSF47413. SSF47413. 1 hit.
PROSITEiView protein in PROSITE
PS50943. HTH_CROC1. 1 hit.

Sequencei

Sequence statusi: Complete.

P23873-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMSFQKIYSP TQLANAMKLV RQQNGWTQSE LAKKIGIKQA TISNFENNPD
60 70 80
NTTLTTFFKI LQSLELSMTL CDAKNASPES TEQQNLEW
Length:88
Mass (Da):10,016
Last modified:November 1, 1991 - v1
Checksum:i63C0E13C1C06CBDA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M61242 Genomic DNA. Translation: AAA56877.1.
U00096 Genomic DNA. Translation: AAC74581.1.
AP009048 Genomic DNA. Translation: BAA15180.1.
PIRiA38112.
RefSeqiNP_416025.1. NC_000913.3.
WP_001301023.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74581; AAC74581; b1508.
BAA15180; BAA15180; BAA15180.
GeneIDi946065.
KEGGiecj:JW1501.
eco:b1508.
PATRICifig|1411691.4.peg.759.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiHIPB_ECOLI
AccessioniPrimary (citable) accession number: P23873
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: November 1, 1991
Last modified: July 5, 2017
This is version 127 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references