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Protein

Serine/threonine-protein kinase toxin HipA

Gene

hipA

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

Functioni

Toxic component of a type II toxin-antitoxin (TA) module, first identified by mutations that increase production of persister cells, a fraction of cells that are phenotypic variants not killed by antibiotics, which lead to multidrug tolerance (PubMed:6348026, PubMed:8021189, PubMed:16707675, PubMed:26222023). Persistence may be ultimately due to global remodeling of the persister cell's ribosomes (PubMed:25425348). Phosphorylates Glu-tRNA-ligase (AC P04805, gltX, on 'Ser-239') in vivo (PubMed:24095282, PubMed:24343429). 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 (p)ppGpp levels, which inhibits replication, transcription, translation and cell wall synthesis, reducing growth and leading to persistence and multidrug resistance (PubMed:24095282, PubMed:24343429, PubMed:25848049). Once the level of HipA exceeds a threshold cells become dormant, and the length of dormancy is determined by how much HipA levels exceed the threshold (PubMed:20616060). 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, as well as cold-sensitivity (PubMed:14622409, PubMed:16707675). Wild-type cells produce persisters at a frequency of 10(-6) to 10(-5) whereas hipA7 cells produce about 100-fold more persisters (PubMed:14622409, PubMed:16707675, PubMed:25425348). hipA7 decreases the affinity for antitoxin HipB, leading to increased HipA levels and persistence (PubMed:20616060); depending on the protein level, can be toxic enough to reduce cell growth or even kill cells. Generation of persister cells requires (p)ppGpp as cells lacking relA or relA/spoT generate fewer or no persister cells respectively compared to hipA7 (PubMed:14622409, PubMed:25848049). Generation of persister cells by HipA also requires mRNA interferase toxins (such as MazF, RelE or YafO) and Lon protease; a strain deleted for 10 type II TAs does not produce persisters when HipA (or HipA7) is expressed, nor does a lon deletion strain or bacteria with alterations of polyphosphate levels, although levels of (p)ppGpp increase (PubMed:25848049). The toxic effect of HipA is neutralized by its cognate antitoxin HipB (PubMed:20616060). Also neutralized by overexpression of gltX (PubMed:24343429, PubMed:28430938). With HipB acts as a corepressor for transcription of the hipBA promoter (PubMed:8021189); binding of HipA-HipB to DNA induces a 70 degree bend (PubMed:19150849, PubMed:26222023). This brings together and dimerizes 2 HipA molecules, which distorts the promoter region, preventing sigma-factor binding; additionally HipA and HipB would physically prevent RNA core polymerase from contacting the -35 promoter box (PubMed:26222023). May play a role in biofilm formation (PubMed:23329678).15 Publications

Miscellaneous

The hipA7 allele (G22S and D291A) as well as a P86L mutation have been identified in E.coli isolates from human patients with urinary tract infections, showing the mutations may be clinically relevant (PubMed:26222023).1 Publication

Catalytic activityi

ATP + a protein = ADP + a phosphoprotein.1 Publication

Enzyme regulationi

Once phosphorylated no longer has kinase activity.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei181ATPCombined sources1 Publication1
Active sitei309Proton acceptor1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi152 – 157ATPCombined sources1 Publication6
Nucleotide bindingi234 – 236ATPCombined sources1 Publication3
Nucleotide bindingi311 – 314ATPCombined sources1 Publication4
Nucleotide bindingi331 – 332ATPCombined sources1 Publication2
DNA bindingi379 – 3821 Publication4

GO - Molecular functioni

  • ATP binding Source: EcoCyc
  • bacterial-type RNA polymerase transcriptional repressor activity, sequence-specific DNA binding Source: CollecTF
  • magnesium ion binding Source: EcoCyc
  • protein serine/threonine kinase activity Source: EcoCyc
  • sequence-specific DNA binding Source: CollecTF
  • toxin activity Source: UniProtKB-KW
  • transcription regulatory region sequence-specific DNA binding Source: CollecTF

GO - Biological processi

  • dormancy process Source: EcoCyc
  • negative regulation of catalytic activity Source: EcoCyc
  • peptidyl-serine autophosphorylation Source: EcoCyc
  • response to antibiotic Source: UniProtKB-KW
  • single-species biofilm formation Source: EcoCyc

Keywordsi

Molecular functionDNA-binding, Kinase, Repressor, Serine/threonine-protein kinase, Transferase
Biological processAntibiotic resistance
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10443-MONOMER.
MetaCyc:EG10443-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Serine/threonine-protein kinase toxin HipA (EC:2.7.11.11 Publication)
Short name:
Ser/Thr-protein kinase HipA
Alternative name(s):
Toxin HipA
Gene namesi
Name:hipA
Ordered Locus Names:b1507, JW1500
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10443. hipA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • protein-DNA complex Source: CollecTF

Pathology & Biotechi

Disruption phenotypei

A hipA or a hipB-hipA operon deletion have no visible phenotype (PubMed:20616060). Initially cells lacking hipA or the hipBA operon were thought not to produce persister cells at a high frequency; this was later shown to be a strain-specific phenotype (PubMed:8021189). 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
Mutagenesisi22G → S: Loss of toxicity, does not confer high persistence. Single mutation has decreased affinity for HipB-operator. Loss of toxicity, high levels of persister cells and cold sensitivity, decreased affinity for HipB; in hipA7; when associated with A-291. 3 Publications1
Mutagenesisi86P → L: High levels of persister cells formed which survive better than wild-type in ampicillin or ciprofloxacin, decreased affinity for HipB-operator. 1 Publication1
Mutagenesisi88D → N: Loss of toxicity, still confers high levels of persister cells. Decreased affinity for HipB-operator. 2 Publications1
Mutagenesisi150S → A: No phosphorylation; cells grow normally. 1 Publication1
Mutagenesisi291D → A: Retains toxicity and high persistence but not cold-sensitive. Loss of toxicity, high levels of persister cells and cold sensitivity, decreased affinity for HipB; in hipA7; when associated with S-22. 2 Publications1
Mutagenesisi309D → Q: Loss of autophosphorylation; cells grow normally; protein can accumulate to high levels in E.coli. 1 Publication1
Mutagenesisi332D → Q: Loss of autophosphorylation; cells grow normally. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000839881 – 440Serine/threonine-protein kinase toxin HipAAdd BLAST440

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei150Phosphoserine; by autocatalysis2 Publications1

Post-translational modificationi

Autophosphorylates intermolecularly on Ser-150; phosphorylated form not seen to bind ATP and no longer has kinase activity.2 Publications

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP23874.
PRIDEiP23874.

PTM databases

iPTMnetiP23874.

Expressioni

Gene expression databases

CollecTFiEXPREG_00000970.

Interactioni

Subunit structurei

Forms a HipA2HipB2 heterotetramer which can interact with a single operator on DNA (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). Mutations present in allele hipA7 (G22S and D291A) decrease the affinity of HipA for HipB (PubMed:20616060).7 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi4260220. 11 interactors.
DIPiDIP-9898N.
IntActiP23874. 4 interactors.
MINTiMINT-1292260.
STRINGi316385.ECDH10B_1638.

Structurei

Secondary structure

1440
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Beta strandi11 – 18Combined sources8
Beta strandi24 – 28Combined sources5
Helixi30 – 34Combined sources5
Beta strandi35 – 37Combined sources3
Beta strandi49 – 52Combined sources4
Helixi55 – 62Combined sources8
Beta strandi65 – 67Combined sources3
Helixi69 – 79Combined sources11
Beta strandi82 – 85Combined sources4
Helixi86 – 93Combined sources8
Beta strandi98 – 100Combined sources3
Beta strandi101 – 104Combined sources4
Beta strandi114 – 116Combined sources3
Beta strandi117 – 119Combined sources3
Helixi122 – 130Combined sources9
Turni131 – 133Combined sources3
Helixi137 – 139Combined sources3
Beta strandi149 – 152Combined sources4
Beta strandi153 – 155Combined sources3
Beta strandi158 – 163Combined sources6
Beta strandi166 – 170Combined sources5
Beta strandi178 – 181Combined sources4
Beta strandi185 – 188Combined sources4
Beta strandi189 – 191Combined sources3
Beta strandi193 – 196Combined sources4
Helixi199 – 212Combined sources14
Beta strandi220 – 225Combined sources6
Beta strandi228 – 234Combined sources7
Beta strandi236 – 240Combined sources5
Beta strandi247 – 249Combined sources3
Beta strandi252 – 254Combined sources3
Helixi255 – 258Combined sources4
Helixi263 – 265Combined sources3
Helixi268 – 270Combined sources3
Helixi275 – 282Combined sources8
Helixi288 – 304Combined sources17
Helixi312 – 314Combined sources3
Beta strandi316 – 319Combined sources4
Helixi321 – 323Combined sources3
Beta strandi325 – 327Combined sources3
Helixi337 – 339Combined sources3
Beta strandi342 – 344Combined sources3
Helixi347 – 349Combined sources3
Beta strandi351 – 358Combined sources8
Beta strandi361 – 365Combined sources5
Helixi366 – 368Combined sources3
Helixi371 – 381Combined sources11
Helixi385 – 407Combined sources23
Beta strandi412 – 414Combined sources3
Helixi416 – 434Combined sources19

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4YG7X-ray3.77D/K2-437[»]
5K98X-ray3.99A/D2-440[»]
ProteinModelPortaliP23874.
SMRiP23874.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP23874.

Family & Domainsi

Sequence similaritiesi

Belongs to the HipA Ser/Thr kinase family.Curated

Phylogenomic databases

eggNOGiENOG4105CAF. Bacteria.
COG3550. LUCA.
HOGENOMiHOG000188799.
InParanoidiP23874.
KOiK07154.

Family and domain databases

InterProiView protein in InterPro
IPR012893. HipA-like_C.
IPR017508. HipA_N1.
PfamiView protein in Pfam
PF13657. Couple_hipA. 1 hit.
PF07804. HipA_C. 1 hit.
TIGRFAMsiTIGR03071. couple_hipA. 1 hit.

Sequencei

Sequence statusi: Complete.

P23874-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPKLVTWMNN QRVGELTKLA NGAHTFKYAP EWLASRYARP LSLSLPLQRG
60 70 80 90 100
NITSDAVFNF FDNLLPDSPI VRDRIVKRYH AKSRQPFDLL SEIGRDSVGA
110 120 130 140 150
VTLIPEDETV THPIMAWEKL TEARLEEVLT AYKADIPLGM IREENDFRIS
160 170 180 190 200
VAGAQEKTAL LRIGNDWCIP KGITPTTHII KLPIGEIRQP NATLDLSQSV
210 220 230 240 250
DNEYYCLLLA KELGLNVPDA EIIKAGNVRA LAVERFDRRW NAERTVLLRL
260 270 280 290 300
PQEDMCQTFG LPSSVKYESD GGPGIARIMA FLMGSSEALK DRYDFMKFQV
310 320 330 340 350
FQWLIGATDG HAKNFSVFIQ AGGSYRLTPF YDIISAFPVL GGTGIHISDL
360 370 380 390 400
KLAMGLNASK GKKTAIDKIY PRHFLATAKV LRFPEVQMHE ILSDFARMIP
410 420 430 440
AALDNVKTSL PTDFPENVVT AVESNVLRLH GRLSREYGSK
Length:440
Mass (Da):49,276
Last modified:July 19, 2003 - v2
Checksum:i378771C4CAB55319
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti40P → Q in AAA56878 (PubMed:1715862).Curated1
Sequence conflicti214 – 215GL → WV in AAA56878 (PubMed:1715862).Curated2
Sequence conflicti274G → R in AAA56878 (PubMed:1715862).Curated1

Mass spectrometryi

Molecular mass is 49143.80 Da from positions 1 - 440. Determined by MALDI. 1 Publication
Molecular mass is 49223.80 Da from positions 1 - 440. Determined by MALDI. Phosphorylated form.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M61242 Genomic DNA. Translation: AAA56878.1.
U00096 Genomic DNA. Translation: AAC74580.1.
AP009048 Genomic DNA. Translation: BAA15179.2.
PIRiF64904.
RefSeqiNP_416024.1. NC_000913.3.
WP_001125439.1. NZ_CP014272.1.

Genome annotation databases

EnsemblBacteriaiAAC74580; AAC74580; b1507.
BAA15179; BAA15179; BAA15179.
GeneIDi946064.
KEGGiecj:JW1500.
eco:b1507.
PATRICifig|1411691.4.peg.760.

Similar proteinsi

Entry informationi

Entry nameiHIPA_ECOLI
AccessioniPrimary (citable) accession number: P23874
Secondary accession number(s): P76139, P76880, P77507
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1991
Last sequence update: July 19, 2003
Last modified: November 22, 2017
This is version 132 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

Has been reported to phosphorylate EF-Tu in vitro (on 'Thr-383') (PubMed:19150849). According to another report, does not phosphorylate EF-Tu (PubMed:19622872).2 Publications

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
  3. SIMILARITY comments
    Index of protein domains and families