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Protein

RNA-binding protein Hfq

Gene

hfq

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

Functioni

RNA chaperone that binds small regulatory RNA (sRNAs) and mRNAs to facilitate mRNA translational regulation in response to envelope stress, environmental stress and changes in metabolite concentrations. Involved in the regulation of stress responses mediated by the sigma factors RpoS, sigma-E and sigma-32 (PubMed:17158661). Binds with high specificity to tRNAs (PubMed:18230766). Binds sRNA antitoxin RalA (PubMed:24748661). In vitro, stimulates synthesis of long tails by poly(A) polymerase I (PubMed:10677490). Required for RNA phage Qbeta replication (PubMed:805130). Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation (PubMed:19909729).6 Publications

GO - Molecular functioni

  • bent DNA binding Source: EcoliWiki
  • RNA binding Source: EcoCyc

GO - Biological processi

  • negative regulation of translation, ncRNA-mediated Source: EcoliWiki
  • positive regulation of translation, ncRNA-mediated Source: EcoCyc
  • regulation of transcription, DNA-templated Source: InterPro

Keywordsi

Molecular functionDNA-binding, RNA-binding
Biological processStress response

Enzyme and pathway databases

BioCyciEcoCyc:EG10438-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
RNA-binding protein HfqUniRule annotation
Alternative name(s):
HF-1
Host factor-I protein
Short name:
HF-I
Gene namesi
Name:hfqUniRule annotation
Ordered Locus Names:b4172, JW4130
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10438 hfq

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

Pathology & Biotechi

Disruption phenotypei

Deletion of hfq seems to lead to a significant translational fidelity problem. Deletion increases persister cell formation (PubMed:19909729). Deletion abolishes the antitoxin activity of sRNA antitoxin RalA, preventing it from neutralizing toxin RalR (PubMed:24748661).2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved3 Publications
ChainiPRO_00000956012 – 102RNA-binding protein HfqAdd BLAST101

Proteomic databases

EPDiP0A6X3
PaxDbiP0A6X3
PRIDEiP0A6X3

Interactioni

Subunit structurei

Homohexamer (PubMed:12853626). Interacts with H-NS (PubMed:11222598).UniRule annotation2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
rhoP0AG305EBI-547637,EBI-545468

Protein-protein interaction databases

BioGridi4261250, 265 interactors
DIPiDIP-36047N
IntActiP0A6X3, 78 interactors
MINTiP0A6X3
STRINGi316385.ECDH10B_4367

Structurei

Secondary structure

1102
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi8 – 17Combined sources10
Beta strandi22 – 26Combined sources5
Beta strandi31 – 39Combined sources9
Beta strandi41 – 55Combined sources15
Helixi56 – 58Combined sources3
Beta strandi59 – 66Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HK9X-ray2.15A/B/C/D/E/F1-72[»]
1M7Cmodel-A/B/C/D/E/F9-76[»]
1OOUmodel-A/B/C/D/E/F6-64[»]
1OOVmodel-A/B/C/D/E/F6-64[»]
2Y90X-ray2.25A1-102[»]
2YHTX-ray2.90A/B/C/D/E/F/G/H/I/J/K/L1-72[»]
3GIBX-ray2.40A/B/C2-69[»]
3QHSX-ray2.85A/B/C/D/E/F/G/H/I/J/K/L1-102[»]
3QO3X-ray2.15A/B/C/D/E/F1-65[»]
3RERX-ray1.70A/B/C/D/E/F1-65[»]
3RESX-ray2.00A/B/C/D/E/F/G/H/I/J/K/L1-65[»]
3VU3X-ray2.85C/D/E/F/G/H1-102[»]
4JRIX-ray1.83A/B/C/D2-69[»]
4JRKX-ray1.89A/B/C2-69[»]
4JUVX-ray2.19A/B/C/D/E/F2-69[»]
4RCBX-ray1.63A5-71[»]
4RCCX-ray1.98A5-71[»]
4V2SX-ray3.48A/B/C/D/E/F1-102[»]
DisProtiDP01050
ProteinModelPortaliP0A6X3
SMRiP0A6X3
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A6X3

Family & Domainsi

Sequence similaritiesi

Belongs to the Hfq family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105KW8 Bacteria
COG1923 LUCA
HOGENOMiHOG000004931
InParanoidiP0A6X3
KOiK03666
OMAiQQMVYKH
PhylomeDBiP0A6X3

Family and domain databases

CDDicd01716 Hfq, 1 hit
HAMAPiMF_00436 Hfq, 1 hit
InterProiView protein in InterPro
IPR005001 Hfq
IPR010920 LSM_dom_sf
PANTHERiPTHR34772 PTHR34772, 1 hit
PfamiView protein in Pfam
PF17209 Hfq, 1 hit
SUPFAMiSSF50182 SSF50182, 1 hit
TIGRFAMsiTIGR02383 Hfq, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A6X3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV
60 70 80 90 100
SQMVYKHAIS TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE

TE
Length:102
Mass (Da):11,166
Last modified:January 23, 2007 - v2
Checksum:iE47FA9B07A39304D
GO

Sequence cautioni

The sequence AAA24175 differs from that shown. Reason: Frameshift at position 72.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D00743 Genomic DNA Translation: BAA00644.1
U14003 Genomic DNA Translation: AAA97068.1
U00096 Genomic DNA Translation: AAC77129.1
AP009048 Genomic DNA Translation: BAE78173.1
M63655 Genomic DNA Translation: AAA24175.1 Frameshift.
U00005 Unassigned DNA Translation: AAC43397.1
PIRiS26832 S56397
RefSeqiNP_418593.1, NC_000913.3
WP_001051883.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC77129; AAC77129; b4172
BAE78173; BAE78173; BAE78173
GeneIDi948689
KEGGiecj:JW4130
eco:b4172
PATRICifig|1411691.4.peg.2529

Similar proteinsi

Entry informationi

Entry nameiHFQ_ECOLI
AccessioniPrimary (citable) accession number: P0A6X3
Secondary accession number(s): O24728
, P25521, Q2M6D3, Q47383
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: January 23, 2007
Last modified: March 28, 2018
This is version 125 of the entry and version 2 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
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Main funding by: National Institutes of Health