P0A6X3 (HFQ_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Protein hfq

Alternative name(s):
HF-1
Host factor-I protein
Short name=HF-I

Gene names

Name:	hfq
Ordered Locus Names:	b4172, JW4130

Organism

Escherichia coli (strain K12)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	102 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Binds with high specificity to tRNAs. In vitro, stimulates synthesis of long tails by poly(A) polymerase I. Required for RNA phage Qbeta replication. Ref.8 Ref.9 Ref.10 Ref.11 Ref.13 Seems to play a role in persister cell formation; upon overexpression decreases persister cell formation while deletion increases persister formation. Ref.8 Ref.9 Ref.10 Ref.11 Ref.13
Subunit structure	Homohexamer.
Disruption phenotype	Deletion of hfq seems to lead to a significant translational fidelity problem. Deletion also increases persister cell formation. Ref.13
Sequence similarities	Belongs to the hfq family.
Sequence caution	The sequence AAA24175.1 differs from that shown. Reason: Frameshift at position 72.

Ontologies

Keywords
Biological process	Stress response
Ligand	DNA-binding RNA-binding
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	negative regulation of translation, ncRNA-mediated Inferred from expression pattern. Source: EcoliWiki regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: InterPro response to stress Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	RNA binding Inferred from electronic annotation. Source: UniProtKB-KW bent DNA binding Inferred from direct assay. Source: EcoliWiki
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.1 Ref.7 Ref.8

Chain

2 – 102

101

Protein hfq HAMAP MF_00436

PRO_0000095601

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

102

Helix Strand Turn

Details...

Helix

8 – 17

10

Beta strand

22 – 26

5

Beta strand

31 – 39

9

Beta strand

41 – 55

15

Helix

56 – 58

3

Beta strand

59 – 66

8

Sequences

	Sequence		Length	Mass (Da)
	P0A6X3 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: E47FA9B07A39304D	FASTA	102	11,166
	10 20 30 40 50 60 MAKGQSLQDP FLNALRRERV PVSIYLVNGI KLQGQIESFD QFVILLKNTV SQMVYKHAIS 70 80 90 100 TVVPSRPVSH HSNNAGGGTS SNYHHGSSAQ NTSAQQDSEE TE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification and sequence determination of the host factor gene for bacteriophage Q beta." Kajitani M., Ishihama A. Nucleic Acids Res. 19:1063-1066(1991) [PubMed: 2020545] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-45.
[2]	"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes." Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R. Nucleic Acids Res. 23:2105-2119(1995) [PubMed: 7610040] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"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 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[4]	"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: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"Structure of Escherichia coli K-12 miaA and characterization of the mutator phenotype caused by miaA insertion mutations." Winkler M.E., Connolly D.M. J. Bacteriol. 173:1711-1721(1991) [PubMed: 1999389] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-79. Strain: K12.
[6]	"The Escherichia coli hflA locus encodes a putative GTP-binding protein and two membrane proteins, one of which contains a protease-like domain." Noble J.A., Innis M.A., Koonin E.V., Rudd K.E., Banuett F., Herskowitz I. Proc. Natl. Acad. Sci. U.S.A. 90:10866-10870(1993) [PubMed: 8248183] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 89-102. Strain: K12.
[7]	"DNA binding properties of the hfq gene product of Escherichia coli." Takada A., Wachi M., Kaidow A., Takamura M., Nagai K. Biochem. Biophys. Res. Commun. 236:576-579(1997) [PubMed: 9245691] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-19, DNA-BINDING.
[8]	"The host factor required for RNA phage Qbeta RNA replication in vitro. Intracellular location, quantitation, and purification by polyadenylate-cellulose chromatography." Carmichael G.G., Weber K., Niveleau A., Wahba A.J. J. Biol. Chem. 250:3607-3612(1975) [PubMed: 805130] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-6, ROLE IN PHAGE QBETA REPLICATION.
[9]	"Host factor Hfq of Escherichia coli stimulates elongation of poly(A) tails by poly(A) polymerase I." Hajnsdorf E., Regnier P. Proc. Natl. Acad. Sci. U.S.A. 97:1501-1505(2000) [PubMed: 10677490] [Abstract] Cited for: ROLE IN ELONGATION OF MRNA POLY(A) TAILS.
[10]	"Hfq is necessary for regulation by the untranslated RNA DsrA." Sledjeski D.D., Whitman C., Zhang A. J. Bacteriol. 183:1997-2005(2001) [PubMed: 11222598] [Abstract] Cited for: FUNCTION IN REGULATORY ACTIVITY OF DSRA.
[11]	"Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli." Guisbert E., Rhodius V.A., Ahuja N., Witkin E., Gross C.A. J. Bacteriol. 189:1963-1973(2007) [PubMed: 17158661] [Abstract] Cited for: FUNCTION IN REGULATION OF STRESS RESPONSE.
[12]	"The RNA binding protein Hfq interacts specifically with tRNAs." Lee T., Feig A.L. RNA 14:514-523(2008) [PubMed: 18230766] [Abstract] Cited for: INTERACTION WITH TRNAS. Strain: K12.
[13]	"Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli." Kim Y., Wood T.K. Biochem. Biophys. Res. Commun. 391:209-213(2010) [PubMed: 19909729] [Abstract] Cited for: FUNCTION IN PERSISTER CELL FORMATION, DISRUPTION PHENOTYPE. Strain: K12 / BW25113.
[14]	"Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli." Sauter C., Basquin J., Suck D. Nucleic Acids Res. 31:4091-4098(2003) [PubMed: 12853626] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 1-72.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

PIR

S56397. S26832.

RefSeq

NP_418593.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1HK9	X-ray	2.15	A/B/C/D/E/F	1-72	[»]
1M7C	model	-	A/B/C/D/E/F	9-76	[»]
1OOU	model	-	A/B/C/D/E/F	6-64	[»]
1OOV	model	-	A/B/C/D/E/F	6-64	[»]
2YHT	X-ray	2.90	A/B/C/D/E/F/G/H/I/J/K/L	1-72	[»]
3GIB	X-ray	2.40	A/B/C	2-69	[»]
3QHS	X-ray	2.85	A/B/C/D/E/F/G/H/I/J/K/L	1-102	[»]
3RER	X-ray	1.70	A/B/C/D/E/F	1-65	[»]
3RES	X-ray	2.00	A/B/C/D/E/F/G/H/I/J/K/L	1-65	[»]

ProteinModelPortal

P0A6X3.

SMR

P0A6X3. Positions 4-71.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-36047N.

IntAct

P0A6X3. 76 interactions.

Proteomic databases

PRIDE

P0A6X3.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000003865; EBESCP00000003865; EBESCG00000003160.
EBESCT00000003866; EBESCP00000003866; EBESCG00000003160.
EBESCT00000003867; EBESCP00000003867; EBESCG00000003160.
EBESCT00000017932; EBESCP00000017223; EBESCG00000016988.

GeneID

948689.

GenomeReviews

Gene locus JW4130 in contig AP009048_GR.
Gene locus b4172 in contig U00096_GR.

KEGG

ecj:JW4130.
eco:b4172.

PATRIC

32123917. VBIEscCol129921_4303.

Organism-specific databases

EchoBASE

EB0433.

EcoGene

EG10438. hfq.

Phylogenomic databases

eggNOG

COG1923.

GeneTree

EBGT00050000011789.

HOGENOM

HBG645207.

OMA

KNTVTQM.

PhylomeDB

P0A6X3.

ProtClustDB

PRK00395.

Enzyme and pathway databases

BioCyc

EcoCyc:EG10438-MONOMER.

Gene expression databases

Genevestigator

P0A6X3.

Family and domain databases

HAMAP

MF_00436. Lsm_Hfq.
[Tree]

InterPro

IPR005001. Hfq.
IPR010920. LSM-related_domain.
IPR001163. LSM_domain.
[Graphical view]

KO

K03666.

Pfam

PF01423. LSM. 1 hit.
[Graphical view]

SUPFAM

SSF50182. Sm_like_riboprot. 1 hit.

TIGRFAMs

TIGR02383. Hfq. 1 hit.

ProtoNet

Search...

Entry information

Entry name

HFQ_ECOLI

Accession

Primary (citable) accession number: P0A6X3
Secondary accession number(s): O24728 , P25521, Q2M6D3, Q47383

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 29, 2005
Last sequence update:	January 23, 2007
Last modified:	January 25, 2012
This is version 74 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program