Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P23874 (HIPA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 109. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Serine/threonine-protein kinase HipA

Short name=Ser/Thr-protein kinase HipA
EC=2.7.11.1
Alternative name(s):
Toxin HipA
Gene names
Name:hipA
Ordered Locus Names:b1507, JW1500
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length440 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Toxic component of a toxin-antitoxin (TA) module. Phosphorylates Glu-tRNA-ligase (GltX, on 'Ser-239') in vivo. Phosphorylation of GltX prevents it from being charged, leading to an increase in uncharged tRNA(Glu). This induces amino acid starvation and the stringent response via RelA/SpoT and increased ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to multidrug resistance and persistence. The hipA7 mutation (a double G22S D291A mutation) leads to increased generation of persister cells, cells that survive antibiotic treatment probably by entering into a dormant state. Wild-type cells produce persisters at a frequency of 10(-6) to 10(-5) whereas mutant hipA7 cells produce persisters at a frequency of 10(-2). Generation of persister cells requires ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7. Low level expression of HipA induces dormancy and depending on the protein level, can be toxic enough to reduce cell growth or even kill cells. Low levels of wild-type HipA lead to high beta-lactam antibiotic tolerance of the survivor cells, also dependent on relA and relA/spoT. The toxic effect of HipA is neutralized by its cognate antitoxin HipB. With HipB acts as a corepressor for transcription of the hipBA promoter; binding to DNA induces a 70 degree bend. Ref.4 Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.11 Ref.13

Catalytic activity

ATP + a protein = ADP + a phosphoprotein.

Enzyme regulation

Once phosphorylated no longer has kinase activity. Ref.14

Subunit structure

Forms a HipA2HipB2 heterotetramer which can interact with DNA. Ref.10 Ref.11 Ref.13

Post-translational modification

Autophosphorylates intermolecularly on Ser-150; phosphorylated form not seen to bind ATP and no longer has kinase activity. Ref.4 Ref.14

Disruption phenotype

Cells lacking hipA or the hipBA operon cannot produce persister cells at a high frequency. Ref.6

Sequence similarities

Belongs to the HipA Ser/Thr kinase family.

Caution

Has been reported to phosphorylate EF-Tu in vitro (on 'Thr-383') (Ref.13). According to another report, does not phosphorylate EF-Tu (Ref.12).

Mass spectrometry

Molecular mass is 49143.80 Da from positions 1 - 440. Determined by MALDI. Ref.11

Molecular mass is 49223.80 Da from positions 1 - 440. Determined by MALDI. Phosphorylated form. Ref.11

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 440440Serine/threonine-protein kinase HipA
PRO_0000083988

Regions

Nucleotide binding152 – 1576ATP
Nucleotide binding234 – 2363ATP
Nucleotide binding311 – 3144ATP
Nucleotide binding331 – 3322ATP
DNA binding379 – 3824 Ref.13

Sites

Active site3091Proton acceptor Probable
Binding site1811ATP

Amino acid modifications

Modified residue1501Phosphoserine; by autocatalysis Ref.4 Ref.14

Experimental info

Mutagenesis221G → S: Loss of toxicity, does not confer high persistence. Loss of toxicity, high persistence and cold sensitivity; in hipA7; when associated with A-291. Ref.7
Mutagenesis881D → N: Loss of toxicity, still confers high persistence. Ref.7
Mutagenesis1501S → A: No phosphorylation; cells grow normally. Ref.4
Mutagenesis2911D → A: Retains toxicity and high persistence but not cold-sensitive. Loss of toxicity, high persistence and cold sensitivity; in hipA7; when associated with S-22. Ref.7
Mutagenesis3091D → Q: Loss of autophosphorylation; cells grow normally; protein can accumulate to high levels in E.coli. Ref.4
Mutagenesis3321D → Q: Loss of autophosphorylation; cells grow normally. Ref.4
Sequence conflict401P → Q in AAA56878. Ref.1
Sequence conflict214 – 2152GL → WV in AAA56878. Ref.1
Sequence conflict2741G → R in AAA56878. Ref.1

Secondary structure

.............................................................................................. 440
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P23874 [UniParc].

Last modified July 19, 2003. Version 2.
Checksum: 378771C4CAB55319

FASTA44049,276
        10         20         30         40         50         60 
MPKLVTWMNN QRVGELTKLA NGAHTFKYAP EWLASRYARP LSLSLPLQRG NITSDAVFNF 

        70         80         90        100        110        120 
FDNLLPDSPI VRDRIVKRYH AKSRQPFDLL SEIGRDSVGA VTLIPEDETV THPIMAWEKL 

       130        140        150        160        170        180 
TEARLEEVLT AYKADIPLGM IREENDFRIS VAGAQEKTAL LRIGNDWCIP KGITPTTHII 

       190        200        210        220        230        240 
KLPIGEIRQP NATLDLSQSV DNEYYCLLLA KELGLNVPDA EIIKAGNVRA LAVERFDRRW 

       250        260        270        280        290        300 
NAERTVLLRL PQEDMCQTFG LPSSVKYESD GGPGIARIMA FLMGSSEALK DRYDFMKFQV 

       310        320        330        340        350        360 
FQWLIGATDG HAKNFSVFIQ AGGSYRLTPF YDIISAFPVL GGTGIHISDL KLAMGLNASK 

       370        380        390        400        410        420 
GKKTAIDKIY PRHFLATAKV LRFPEVQMHE ILSDFARMIP AALDNVKTSL PTDFPENVVT 

       430        440 
AVESNVLRLH GRLSREYGSK 

« Hide

References

« Hide 'large scale' references
[1]"Structure and organization of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis."
Black D.S., Kelly A.J., Mardis M.J., Moyed H.S.
J. Bacteriol. 173:5732-5739(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"Kinase activity of overexpressed HipA is required for growth arrest and multidrug tolerance in Escherichia coli."
Correia F.F., D'Onofrio A., Rejtar T., Li L., Karger B.L., Makarova K., Koonin E.V., Lewis K.
J. Bacteriol. 188:8360-8367(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 134-157, FUNCTION AS A KINASE, ACTIVE SITE, PHOSPHORYLATION AT SER-150, ANTIBIOTIC TOLERANCE, MUTAGENESIS OF SER-150; ASP-309 AND ASP-332.
Strain: K12.
[5]"hipA, a newly recognized gene of Escherichia coli K-12 that affects frequency of persistence after inhibition of murein synthesis."
Moyed H.S., Bertrand K.P.
J. Bacteriol. 155:768-775(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTANT HIPA7 ISOLATION, ROLE IN ANTIBIOTIC TOLERANCE, ROLE IN PERSISTENCE.
Strain: K12.
[6]"Autoregulation of hip, an operon that affects lethality due to inhibition of peptidoglycan or DNA synthesis."
Black D.S., Irwin B., Moyed H.S.
J. Bacteriol. 176:4081-4091(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A TOXIN, DISRUPTION PHENOTYPE.
Strain: K12.
[7]"Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis."
Korch S.B., Henderson T.A., Hill T.M.
Mol. Microbiol. 50:1199-1213(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A TOXIN, FUNCTION IN PERSISTENCE, REQUIREMENT FOR (P)PPGPP, MUTAGENESIS OF GLY-22; ASP-88 AND ASP-291.
Strain: K12 / MG1655 / ATCC 47076.
[8]"Ectopic overexpression of wild-type and mutant hipA genes in Escherichia coli: effects on macromolecular synthesis and persister formation."
Korch S.B., Hill T.M.
J. Bacteriol. 188:3826-3836(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION AS A TOXIN.
Strain: K12 / MG1655 / ATCC 47076.
[9]"HipA-triggered growth arrest and beta-lactam tolerance in Escherichia coli are mediated by RelA-dependent ppGpp synthesis."
Bokinsky G., Baidoo E.E., Akella S., Burd H., Weaver D., Alonso-Gutierrez J., Garcia-Martin H., Lee T.S., Keasling J.D.
J. Bacteriol. 195:3173-3182(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ROLE IN PPGPP RESPONSE.
[10]"Interaction investigations of HipA binding to HipB dimer and HipB dimer + DNA complex: a molecular dynamics simulation study."
Li C., Wang Y., Wang Y., Chen G.
J. Mol. Recognit. 26:556-567(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBUNIT, MODELING OF INTERACTION.
[11]"Molecular mechanism of bacterial persistence by HipA."
Germain E., Castro-Roa D., Zenkin N., Gerdes K.
Mol. Cell 52:248-254(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH HIPB, SUBUNIT, MASS SPECTROMETRY.
Strain: K12 / MG1655 / ATCC 47076.
[12]"New kinase regulation mechanism found in HipBA: a bacterial persistence switch."
Evdokimov A., Voznesensky I., Fennell K., Anderson M., Smith J.F., Fisher D.A.
Acta Crystallogr. D 65:875-879(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH HIPB.
Strain: K12 / DH5-alpha.
[13]"Molecular mechanisms of HipA-mediated multidrug tolerance and its neutralization by HipB."
Schumacher M.A., Piro K.M., Xu W., Hansen S., Lewis K., Brennan R.G.
Science 323:396-401(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS) ALONE AND IN COMPLEX WITH MG-ATP AND HIPB, FUNCTION AS A KINASE, ATP-BINDING, DNA-BINDING, SUBSTRATE, SUBUNIT.
[14]"Role of unusual P loop ejection and autophosphorylation in HipA-mediated persistence and multidrug tolerance."
Schumacher M.A., Min J., Link T.M., Guan Z., Xu W., Ahn Y.H., Soderblom E.J., Kurie J.M., Evdokimov A., Moseley M.A., Lewis K., Brennan R.G.
Cell Rep. 2:518-525(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) PHOSPHORYLATED AND NON-PHOSPHORYLATED AND IN COMPLEX WITH ATP, ATP-BINDING, ENZYME REGULATION, PHOSPHORYLATION AT SER-150.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M61242 Genomic DNA. Translation: AAA56878.1.
U00096 Genomic DNA. Translation: AAC74580.1.
AP009048 Genomic DNA. Translation: BAA15179.2.
PIRF64904.
RefSeqNP_416024.1. NC_000913.3.
YP_489771.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2WIUX-ray2.35A/C1-440[»]
3DNTX-ray1.66A/B1-440[»]
3DNUX-ray1.54A1-440[»]
3DNVX-ray2.68A1-440[»]
3FBRX-ray3.50A1-437[»]
3HZIX-ray2.98A1-440[»]
3TPBX-ray1.88A1-440[»]
3TPDX-ray1.50A1-440[»]
3TPEX-ray1.90A1-440[»]
3TPTX-ray2.25A/B1-440[»]
3TPVX-ray2.30B1-440[»]
ProteinModelPortalP23874.
SMRP23874. Positions 2-437.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-9898N.
IntActP23874. 3 interactions.
MINTMINT-1292260.
STRING511145.b1507.

PTM databases

PhosSiteP0612176.

Proteomic databases

PaxDbP23874.
PRIDEP23874.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74580; AAC74580; b1507.
BAA15179; BAA15179; BAA15179.
GeneID12931226.
946064.
KEGGecj:Y75_p1482.
eco:b1507.
PATRIC32118308. VBIEscCol129921_1574.

Organism-specific databases

EchoBASEEB0438.
EcoGeneEG10443. hipA.

Phylogenomic databases

eggNOGCOG3550.
HOGENOMHOG000188799.
KOK07154.
OMASGAKYES.
OrthoDBEOG6ZSP44.

Enzyme and pathway databases

BioCycEcoCyc:EG10443-MONOMER.
ECOL316407:JW1500-MONOMER.
MetaCyc:EG10443-MONOMER.

Gene expression databases

GenevestigatorP23874.

Family and domain databases

InterProIPR012893. HipA-like_C.
IPR017508. HipA_N1.
IPR012894. HipA_N2.
[Graphical view]
PfamPF13657. Couple_hipA. 1 hit.
PF07804. HipA_C. 1 hit.
PF07805. HipA_N. 1 hit.
[Graphical view]
TIGRFAMsTIGR03071. couple_hipA. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP23874.
PROP23874.

Entry information

Entry nameHIPA_ECOLI
AccessionPrimary (citable) accession number: P23874
Secondary accession number(s): P76139, P76880, P77507
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: July 19, 2003
Last modified: June 11, 2014
This is version 109 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene