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Protein

RNA-binding protein Hfq

Gene

hfq

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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
Complete GO annotation...

Keywords - Biological processi

Stress response

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10438-MONOMER.
ECOL316407:JW4130-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10438. hfq.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

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)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved3 Publications
Chaini2 – 102101RNA-binding protein HfqPRO_0000095601Add
BLAST

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
rhoP0AG304EBI-547637,EBI-545468

Protein-protein interaction databases

BioGridi4261250. 247 interactions.
DIPiDIP-36047N.
IntActiP0A6X3. 77 interactions.
MINTiMINT-8200668.
STRINGi511145.b4172.

Structurei

Secondary structure

1
102
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi8 – 1710Combined sources
Beta strandi22 – 265Combined sources
Beta strandi31 – 399Combined sources
Beta strandi41 – 5515Combined sources
Helixi56 – 583Combined sources
Beta strandi59 – 668Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP0A6X3.
SMRiP0A6X3. Positions 4-71.
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.
OMAiRDGHAQL.
PhylomeDBiP0A6X3.

Family and domain databases

HAMAPiMF_00436. Hfq. 1 hit.
InterProiIPR005001. Hfq.
IPR010920. LSM_dom.
[Graphical view]
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.
PATRICi32123917. VBIEscCol129921_4303.

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliP0A6X3.
SMRiP0A6X3. Positions 4-71.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261250. 247 interactions.
DIPiDIP-36047N.
IntActiP0A6X3. 77 interactions.
MINTiMINT-8200668.
STRINGi511145.b4172.

Proteomic databases

EPDiP0A6X3.
PaxDbiP0A6X3.
PRIDEiP0A6X3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77129; AAC77129; b4172.
BAE78173; BAE78173; BAE78173.
GeneIDi948689.
KEGGiecj:JW4130.
eco:b4172.
PATRICi32123917. VBIEscCol129921_4303.

Organism-specific databases

EchoBASEiEB0433.
EcoGeneiEG10438. hfq.

Phylogenomic databases

eggNOGiENOG4105KW8. Bacteria.
COG1923. LUCA.
HOGENOMiHOG000004931.
InParanoidiP0A6X3.
KOiK03666.
OMAiRDGHAQL.
PhylomeDBiP0A6X3.

Enzyme and pathway databases

BioCyciEcoCyc:EG10438-MONOMER.
ECOL316407:JW4130-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0A6X3.
PROiP0A6X3.

Family and domain databases

HAMAPiMF_00436. Hfq. 1 hit.
InterProiIPR005001. Hfq.
IPR010920. LSM_dom.
[Graphical view]
SUPFAMiSSF50182. SSF50182. 1 hit.
TIGRFAMsiTIGR02383. Hfq. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiHFQ_ECOLI
AccessioniPrimary (citable) accession number: P0A6X3
Secondary accession number(s): O24728
, P25521, Q2M6D3, Q47383
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 29, 2005
Last sequence update: January 23, 2007
Last modified: September 7, 2016
This is version 113 of the entry and version 2 of the sequence. [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
  3. SIMILARITY comments
    Index of protein domains and families

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.