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Protein

DNA-binding protein H-NS

Gene

hns

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

Functioni

A DNA-binding protein implicated in transcriptional repression (silencing) (PubMed:333393, PubMed:2128918, PubMed:8890170, PubMed:8913298, PubMed:9398522, PubMed:16963779, PubMed:17046956, PubMed:23543115). Also involved in bacterial chromosome organization and compaction (PubMed:6379600, PubMed:10982869, PubMed:21903814). H-NS binds tightly to AT-rich dsDNA and inhibits transcription (PubMed:2512122, PubMed:16963779, PubMed:17435766, PubMed:17881364, PubMed:23543115). Binds upstream and downstream of initiating RNA polymerase, trapping it in a loop and preventing transcription (PubMed:11714691). Binds to hundreds of sites, approximately half its binding sites are in non-coding DNA, which only accounts for about 10% of the genome (PubMed:16963779, PubMed:17046956, PubMed:23543115). Many of these loci were horizontally transferred (HTG); this offers the selective advantage of silencing foreign DNA while keeping it in the genome in case of need (PubMed:17046956, PubMed:17881364, PubMed:26789284). Suppresses transcription at many intragenic sites as well as transcription of spurious, non-coding RNAs genome-wide (PubMed:24449106). Repression of HTG by H-NS is thought to allow their DNA to evolve faster than non-H-NS-bound regions, and facilitates integration of HTG into transcriptional regulatory networks (PubMed:26789284). A subset of H-NS/StpA-regulated genes also require Hha (and/or Cnu, ydgT) for repression; Hha and Cnu increase the number of genes DNA bound by H-NS/StpA and may also modulate the oligomerization of the H-NS/StpA-complex (PubMed:23543115). The protein forms 2 clusters in the nucleoid which gather hns-bound loci together, bridging non-contiguous DNA, and causes DNA substantial condensation (PubMed:21903814). Binds DNA better at low temperatures than at 37 degrees Celsius; AT-rich sites nucleate H-NS binding, further DNA-binding is cooperative and this cooperativity decreases with rising temperature (PubMed:17435766, PubMed:17881364). Transcriptional repression can be inhibited by dominant-negative mutants of StpA or itself (PubMed:8755860). May effect transcriptional elongation (PubMed:25638302). Can increase translational efficiency of mRNA with suboptimal Shine-Dalgarno sequences (PubMed:20595230). Plays a role in the thermal control of pili and adhesive curli fimbriae production, by inducing transcription of csgD (PubMed:17010156). Plays a role in flagellar function (PubMed:11031114). Represses the CRISPR-cas promoters, permits only weak transcription of the crRNA precursor; its repression is antagonized by LeuO (PubMed:20132443, PubMed:20659289). Binds preferentially to the upstream region of its own gene recognizing two segments of DNA on both sides of a bend centered around -150 (PubMed:7934818). Overexpression suppresses secY24, a temperature-sensitive mutation (PubMed:1537791). Has also been reported to activate transcription of some genes (PubMed:4566454, PubMed:338303, PubMed:2128918).1 Publication27 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei12Interacts with Hha1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi112 – 117By similarity6

GO - Molecular functioni

  • bent DNA binding Source: EcoliWiki
  • identical protein binding Source: IntAct
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

Transcription, Transcription regulation, Translation regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:PD00288.
ECOL316407:JW1225-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-binding protein H-NS1 Publication
Alternative name(s):
Heat-stable nucleoid-structuring protein1 Publication
Histone-like protein HLP-II
Protein B11 Publication
Protein H11 Publication
Gene namesi
Name:hns1 Publication
Synonyms:bglY1 Publication, cur, drdX1 Publication, hnsA, msyA1 Publication, osmZ1 Publication, pilG, topS
Ordered Locus Names:b1237, JW1225
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10457. hns.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • membrane Source: UniProtKB
  • nucleoid Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Decreased growth below 30 degrees Celsius (PubMed:1691451). Altered expression of a number of genes (PubMed:2128918, PubMed:8890170, PubMed:8913298, PubMed:23543115). Derepression of the cryptic blg operon (PubMed:8913298, PubMed:11790731). Alteration of chromosome organization (PubMed:21903814). Double hns-stpA mutants grow slower and have reduced viable cell counts compared to single hns mutants in MC1029 and MC4100 backgrounds (PubMed:8890170). In 0.3M NaCl a double hns-stpA deletion up-regulates 583 and down-regulates 86 genes, 363 of which are thought to have been horizontally acquired; 131 are also up-regulated in a double cnu-hha deletion (PubMed:23543115). At 28 degrees Celsius csgD transcription is reduced (PubMed:17010156). Flagella loss due to reduced expression of the flhDC operon (PubMed:11031114). Flagella can be restored by expression of flhDC, but strains are non-motile, suggesting H-NS also plays a role in flagellar function (PubMed:11031114). Disruption leads to increased expression of CRISPR-cas genes and increased viral resistance (PubMed:20659289).10 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi2 – 69Missing : No longer complements a deletion mutant, has no dominant-negative effects on wild-type protein, does not oligomerize. 1 PublicationAdd BLAST68
Mutagenesisi2 – 20Missing : No longer complements a deletion mutant, has dominant-negative effects on wild-type protein, oligomerizes. 1 PublicationAdd BLAST19
Mutagenesisi6K → P: No effect on oligomerization of N-terminal fragment 1-89. 1 Publication1
Mutagenesisi12 – 15RTLR → ERLA: Decreased DNA-binding, loss of preference for curved DNA. 1 Publication4
Mutagenesisi12R → C: Derepression of proV and bgl expression, normal DNA-binding, normal oligomerization. 1 Publication1
Mutagenesisi12R → H: Derepression of proV and bgl expression, normal DNA-binding, normal oligomerization. Fragments 1-46 and 1-64 no longer bind Hha. 2 Publications1
Mutagenesisi12R → K: Abolishes the interaction with Hha. 1 Publication1
Mutagenesisi15R → C: Derepression of proV and bgl expression. 1 Publication1
Mutagenesisi15R → H: Derepression of proV and bgl expression. Fragments 1-46 and 1-64 fold incorrectly but still bind Hha. 2 Publications1
Mutagenesisi17Q → P: Abolishes oligomerization of N-terminal fragment 1-89. 1 Publication1
Mutagenesisi26L → P: Partial loss of repressor function. 1 Publication1
Mutagenesisi30L → A or K: Wild-type function. 1 Publication1
Mutagenesisi30L → D: Derepression of proV and partial derepression of bgl epxression, does not dimerize, anomalous protein mobility on gels. 1 Publication1
Mutagenesisi30L → P: Derepression of proV and bgl epxression, does not dimerize, anomalous protein mobility on gels. Protein localizes to nucleoid but no longer forms discreet compact clusters. 2 Publications1
Mutagenesisi32K → Q: Loss of Hha binding by fragment 1-64, protein folding is unaffected. 1 Publication1
Mutagenesisi53 – 55ERT → GRP: Partial loss of repressor function. 1 Publication3
Mutagenesisi54R → C: Derepression of proV and bgl expression. 1 Publication1
Mutagenesisi64 – 137Missing : No longer complements a deletion mutant, has dominant-negative effects on wild-type protein, oligomerizes. 2 PublicationsAdd BLAST74
Mutagenesisi90R → C or H: Derepression of proV expression. 1 Publication1
Mutagenesisi91A → T: Derepression of proV expression. 1 Publication1
Mutagenesisi92 – 137Missing : Derepression of proV expression, loss of DNA-binding, increased oligomerization. No longer complements a deletion mutant, has dominant-negative effects on wild-type protein, oligomerizes. 2 PublicationsAdd BLAST46
Mutagenesisi93R → C: Derepression of proV expression. 1 Publication1
Mutagenesisi94P → L or S: Derepression of proV expression. 1 Publication1
Mutagenesisi95A → T: Derepression of proV expression. 1 Publication1
Mutagenesisi97Y → C, H or S: Partial loss of repressor function. 1 Publication1
Mutagenesisi110T → A: Partial loss of repressor function. 1 Publication1
Mutagenesisi110T → I: Derepression of proV expression. 1 Publication1
Mutagenesisi111G → D or S: Derepression of proV expression. 1 Publication1
Mutagenesisi113G → D: Derepression of proV expression, decreased DNA-binding but still prefers curved DNA, increased oligomerization. 1 Publication1
Mutagenesisi113G → S: Partial loss of repressor function. 1 Publication1
Mutagenesisi114R → C or H: Derepression of proV expression. 1 Publication1
Mutagenesisi115T → I: Derepression of proV expression. 1 Publication1
Mutagenesisi116P → S: Partial loss of repressor function. Protein localizes to nucleoid but forms about 20-fold fewer localization points. 2 Publications1
Mutagenesisi119I → T: Partial loss of repressor function. 1 Publication1
Mutagenesisi122 – 137AMDEQ…FLIKQ → KQWMRKVNPSTIS: Partial loss of repressor function. 1 PublicationAdd BLAST16
Mutagenesisi133F → S: Partial loss of repressor function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved9 Publications
ChainiPRO_00001685032 – 137DNA-binding protein H-NSAdd BLAST136

Post-translational modificationi

Cells (strain MRE-600) in mid-exponential phase have three 15.5 kDa proteins with 3 different isoelectric points; the major form (H1a, pI 7.5) rises in concentration during growth while the 2 minor forms (H1b, pI about 7.2 and H1c, pI 7.0) remain approximately constant (PubMed:6379600).1 Publication

Proteomic databases

EPDiP0ACF8.
PaxDbiP0ACF8.
PRIDEiP0ACF8.

2D gel databases

SWISS-2DPAGEP0ACF8.

Expressioni

Inductioni

Protein levels rise from about 4,000/cell in exponential phase to about 18,000/cell in late stationary phase (at protein level) (PubMed:6379600). Subject to transcriptional auto-repression (PubMed:7934818). Induced by increased hydrostatic pressure (PubMed:8226663). hns transcription can be repressed by overexpressed StpA (which is usually repressed by hns) (PubMed:8890170).4 Publications

Gene expression databases

CollecTFiEXPREG_00000830.

Interactioni

Subunit structurei

Homodimer, also found as tetramers or higher oligomers (PubMed:4566454, PubMed:338303, PubMed:3135462, PubMed:8913298, PubMed:9398522, PubMed:8755860, PubMed:12460581, PubMed:23601147). Oligomerizes into higher-order complexes that form bridges between adjacent DNA helices. The N-terminal region (residues 1-64) can interact with overexpressed StpA (PubMed:8755860). Forms a complex with Cnu (YdgT) (PubMed:21600204). The H-NS dimer forms a heterotrimeric complex with Hha in the absence of DNA; this is mediated by residues 1-46 (PubMed:21600204, PubMed:11790731, PubMed:16650431, PubMed:26085102). Interacts with Hfq (PubMed:2020545).1 Publication12 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
itself10EBI-544934,EBI-544934
cnuP644672EBI-544934,EBI-551907
hhaP0ACE35EBI-544934,EBI-1122578
stpAP0ACG13EBI-544934,EBI-551928

GO - Molecular functioni

  • identical protein binding Source: IntAct

Protein-protein interaction databases

BioGridi4263496. 32 interactors.
850196. 1 interactor.
DIPiDIP-35853N.
IntActiP0ACF8. 49 interactors.
MINTiMINT-1223907.
STRINGi511145.b1237.

Structurei

Secondary structure

1137
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 7Combined sources5
Helixi10 – 17Combined sources8
Turni18 – 20Combined sources3
Helixi24 – 51Combined sources28
Beta strandi97 – 99Combined sources3
Beta strandi100 – 106Combined sources7
Turni110 – 113Combined sources4
Beta strandi115 – 117Combined sources3
Helixi118 – 125Combined sources8
Helixi130 – 132Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HNRNMR-A91-137[»]
1HNSNMR-A91-137[»]
1LR1NMR-A/B2-58[»]
1NI8NMR-A/B2-47[»]
2MW2NMR-B/C1-47[»]
ProteinModelPortaliP0ACF8.
SMRiP0ACF8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0ACF8.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni21 – 63Involved in dimerization1 PublicationAdd BLAST43
Regioni92 – 137Required for DNA-binding1 PublicationAdd BLAST46

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili22 – 492 PublicationsAdd BLAST28

Domaini

A central region (about residues 21-47) is involved in dimerization, but multimerization requires other residues (PubMed:8755860, PubMed:9398522, PubMed:16650431, PubMed:12460581, PubMed:12592399). The dimerization domain (1-47) also acts as a hinge; changes in its structure probably impact oligomerization and DNA-binding geometries (PubMed:23601147). The N-terminus also interacts with Hha, perhaps via residues 2-18; a well-folded dimer is not necessary for Hha binding (PubMed:16650431). The C-terminus (residues 92-137) binds DNA (PubMed:8913298). Residues in the N-terminus contribute to DNA-binding and to discrimination between curved and non-curved DNA (PubMed:12592399).7 Publications

Sequence similaritiesi

Belongs to the histone-like protein H-NS family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiENOG4108SAU. Bacteria.
COG2916. LUCA.
HOGENOMiHOG000218473.
KOiK03746.
OMAiNGVEKTW.

Family and domain databases

Gene3Di1.10.287.1050. 1 hit.
4.10.430.10. 1 hit.
InterProiIPR027444. H-NS_C_dom.
IPR001801. Histone_HNS.
IPR027454. Histone_HNS_oligo_dom.
[Graphical view]
PfamiPF00816. Histone_HNS. 1 hit.
[Graphical view]
PIRSFiPIRSF002096. HnS. 1 hit.
SMARTiSM00528. HNS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P0ACF8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEALKILNN IRTLRAQARE CTLETLEEML EKLEVVVNER REEESAAAAE
60 70 80 90 100
VEERTRKLQQ YREMLIADGI DPNELLNSLA AVKSGTKAKR AQRPAKYSYV
110 120 130
DENGETKTWT GQGRTPAVIK KAMDEQGKSL DDFLIKQ
Length:137
Mass (Da):15,540
Last modified:January 23, 2007 - v2
Checksum:iE628184AC7C86F49
GO

Mass spectrometryi

Molecular mass is 15407.8 Da from positions 2 - 137. Determined by MALDI. A second experiment gave a mass of 15410.1.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07688 Genomic DNA. Translation: CAA30530.1.
X59940 Genomic DNA. Translation: CAA42565.1.
X57231 Genomic DNA. Translation: CAA40507.1.
X67326 Genomic DNA. Translation: CAA47740.1.
Y00976 Genomic DNA. Translation: CAA68786.1.
U00096 Genomic DNA. Translation: AAC74319.1.
AP009048 Genomic DNA. Translation: BAA36117.1.
PIRiS00903.
RefSeqiNP_415753.1. NC_000913.3.
WP_001287378.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74319; AAC74319; b1237.
BAA36117; BAA36117; BAA36117.
GeneIDi945829.
KEGGiecj:JW1225.
eco:b1237.
PATRICi32117730. VBIEscCol129921_1285.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X07688 Genomic DNA. Translation: CAA30530.1.
X59940 Genomic DNA. Translation: CAA42565.1.
X57231 Genomic DNA. Translation: CAA40507.1.
X67326 Genomic DNA. Translation: CAA47740.1.
Y00976 Genomic DNA. Translation: CAA68786.1.
U00096 Genomic DNA. Translation: AAC74319.1.
AP009048 Genomic DNA. Translation: BAA36117.1.
PIRiS00903.
RefSeqiNP_415753.1. NC_000913.3.
WP_001287378.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1HNRNMR-A91-137[»]
1HNSNMR-A91-137[»]
1LR1NMR-A/B2-58[»]
1NI8NMR-A/B2-47[»]
2MW2NMR-B/C1-47[»]
ProteinModelPortaliP0ACF8.
SMRiP0ACF8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263496. 32 interactors.
850196. 1 interactor.
DIPiDIP-35853N.
IntActiP0ACF8. 49 interactors.
MINTiMINT-1223907.
STRINGi511145.b1237.

2D gel databases

SWISS-2DPAGEP0ACF8.

Proteomic databases

EPDiP0ACF8.
PaxDbiP0ACF8.
PRIDEiP0ACF8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74319; AAC74319; b1237.
BAA36117; BAA36117; BAA36117.
GeneIDi945829.
KEGGiecj:JW1225.
eco:b1237.
PATRICi32117730. VBIEscCol129921_1285.

Organism-specific databases

EchoBASEiEB0452.
EcoGeneiEG10457. hns.

Phylogenomic databases

eggNOGiENOG4108SAU. Bacteria.
COG2916. LUCA.
HOGENOMiHOG000218473.
KOiK03746.
OMAiNGVEKTW.

Enzyme and pathway databases

BioCyciEcoCyc:PD00288.
ECOL316407:JW1225-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0ACF8.
PROiP0ACF8.

Gene expression databases

CollecTFiEXPREG_00000830.

Family and domain databases

Gene3Di1.10.287.1050. 1 hit.
4.10.430.10. 1 hit.
InterProiIPR027444. H-NS_C_dom.
IPR001801. Histone_HNS.
IPR027454. Histone_HNS_oligo_dom.
[Graphical view]
PfamiPF00816. Histone_HNS. 1 hit.
[Graphical view]
PIRSFiPIRSF002096. HnS. 1 hit.
SMARTiSM00528. HNS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiHNS_ECOLI
AccessioniPrimary (citable) accession number: P0ACF8
Secondary accession number(s): P08936, Q47267
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 101 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.