Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

RNA polymerase sigma factor RpoH

Gene

rpoH

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

Functioni

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is involved in regulation of expression of heat shock genes. Intracellular concentration of free RpoH protein increases in response to heat shock, which causes association with RNA polymerase (RNAP) and initiation of transcription of heat shock genes, including numerous global transcriptional regulators and genes involved in maintaining membrane functionality and homeostasis. RpoH is then quickly degraded, leading to a decrease in the rate of synthesis of heat shock proteins and shut-off of the heat shock response.UniRule annotation5 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi253 – 27220H-T-H motifUniRule annotationAdd
BLAST

GO - Molecular functioni

  • DNA binding Source: EcoliWiki
  • sigma factor activity Source: EcoCyc
  • transcription factor activity, core RNA polymerase binding Source: CACAO
  • transcription factor activity, sequence-specific DNA binding Source: InterPro
  • zinc ion binding Source: InterPro

GO - Biological processi

  • regulation of gene expression Source: EcoCyc
  • regulation of transcription, DNA-templated Source: EcoliWiki
  • response to heat Source: EcoCyc
  • sporulation resulting in formation of a cellular spore Source: InterPro
  • transcription, DNA-templated Source: CACAO
  • transcription from bacterial-type RNA polymerase promoter Source: EcoCyc
  • transcription initiation from bacterial-type RNA polymerase promoter Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Sigma factor

Keywords - Biological processi

Stress response, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:RPOH-MONOMER.
ECOL316407:JW3426-MONOMER.
MetaCyc:RPOH-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor RpoHUniRule annotation
Alternative name(s):
Heat shock regulatory protein F33.4
RNA polymerase sigma-32 factorUniRule annotation
Gene namesi
Name:rpoHUniRule annotation
Synonyms:fam, hin, htpR
Ordered Locus Names:b3461, JW3426
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10897. rpoH.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • plasma membrane Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Mutants exhibit an increased sensitivity to heat shock but only in the exponential phase of aerobic growth.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi80 – 801Q → N or R: Decrease in activity. Exhibits reduced affinity for core RNAP. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 284284RNA polymerase sigma factor RpoHPRO_0000093957Add
BLAST

Proteomic databases

PaxDbiP0AGB3.
PRIDEiP0AGB3.

Expressioni

Inductioni

Subject to complex regulation at multiple levels (transcription, translation, regulation of activity and degradation). In the absence of heat shock, or after heat shock, activity is inhibited by transient association with DnaK and DnaJ, which reduces the amounts of free active RpoH, makes it unstable and mediates its degradation by the FtsH protease. During heat shock, the intracellular concentration of RpoH increases, due to slightly increased transcription, increased synthesis and stabilization of the protein. Induction occurs mainly at the post-transcriptional level, via translational thermoregulation: at low temperature, the structure of the rpoH mRNA blocks its translation, while at high temperature, melting of the mRNA secondary structure facilitates ribosome binding and synthesis of the RpoH protein. In addition, during heat shock, stabilization of RpoH is triggered by the titration of free DnaK/DnaJ by stress-induced misfolded proteins. Can also be induced by other stress conditions, including during the first round of cell division.9 Publications

Interactioni

Subunit structurei

Interacts with the RNA polymerase core enzyme. Interacts with DnaK and DnaJ.UniRule annotation2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
dnaKP0A6Y85EBI-555342,EBI-542092
groLP0A6F52EBI-555342,EBI-543750

Protein-protein interaction databases

BioGridi4262497. 257 interactions.
DIPiDIP-46203N.
IntActiP0AGB3. 14 interactions.
STRINGi511145.b3461.

Structurei

3D structure databases

ProteinModelPortaliP0AGB3.
SMRiP0AGB3. Positions 35-279.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni53 – 12270Sigma-70 factor domain-2UniRule annotationAdd
BLAST
Regioni228 – 28053Sigma-70 factor domain-4UniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi77 – 804Interaction with polymerase core subunit RpoC

Domaini

The sigma-70 factor domain-2 mediates sequence-specific interaction with the -10 element in promoter DNA, and plays an important role in melting the double-stranded DNA and the formation of the transcription bubble. The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC (By similarity).By similarity
The sigma-70 factor domain-4 contains a helix-turn-helix (H-T-H) motif that mediates interaction with the -35 element in promoter DNA. The domain also mediates interaction with the RNA polymerase subunit RpoA (By similarity).By similarity

Sequence similaritiesi

Belongs to the sigma-70 factor family. RpoH subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DEK. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270269.
InParanoidiP0AGB3.
KOiK03089.
OMAiLNNDEVH.
PhylomeDBiP0AGB3.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_00961. Sigma70_RpoH. 1 hit.
InterProiIPR014284. RNA_pol_sigma-70_dom.
IPR000943. RNA_pol_sigma70.
IPR007627. RNA_pol_sigma70_r2.
IPR007630. RNA_pol_sigma70_r4.
IPR016263. RNA_pol_sigma_factor.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR012759. RNA_pol_sigma_RpoH_proteobac.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04542. Sigma70_r2. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PIRSFiPIRSF000770. RNA_pol_sigma-SigE/K. 1 hit.
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 1 hit.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02392. rpoH_proteo. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0AGB3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDKMQSLAL APVGNLDSYI RAANAWPMLS ADEERALAEK LHYHGDLEAA
60 70 80 90 100
KTLILSHLRF VVHIARNYAG YGLPQADLIQ EGNIGLMKAV RRFNPEVGVR
110 120 130 140 150
LVSFAVHWIK AEIHEYVLRN WRIVKVATTK AQRKLFFNLR KTKQRLGWFN
160 170 180 190 200
QDEVEMVARE LGVTSKDVRE MESRMAAQDM TFDLSSDDDS DSQPMAPVLY
210 220 230 240 250
LQDKSSNFAD GIEDDNWEEQ AANRLTDAMQ GLDERSQDII RARWLDEDNK
260 270 280
STLQELADRY GVSAERVRQL EKNAMKKLRA AIEA
Length:284
Mass (Da):32,469
Last modified:December 20, 2005 - v1
Checksum:i628A17B4C835D00A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti185 – 1851S → A in AAA23991 (PubMed:6387714).Curated
Sequence conflicti193 – 1942QP → HA in AAA23991 (PubMed:6387714).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M20668 Genomic DNA. Translation: AAA24587.1.
J05516 Genomic DNA. No translation available.
K02177 Genomic DNA. Translation: AAA23991.1.
U00039 Genomic DNA. Translation: AAB18436.1.
U00096 Genomic DNA. Translation: AAC76486.1.
AP009048 Genomic DNA. Translation: BAE77832.1.
PIRiH65142. RGECH.
RefSeqiNP_417918.1. NC_000913.3.
WP_000130217.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76486; AAC76486; b3461.
BAE77832; BAE77832; BAE77832.
GeneIDi947970.
KEGGiecj:JW3426.
eco:b3461.
PATRICi32122366. VBIEscCol129921_3560.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M20668 Genomic DNA. Translation: AAA24587.1.
J05516 Genomic DNA. No translation available.
K02177 Genomic DNA. Translation: AAA23991.1.
U00039 Genomic DNA. Translation: AAB18436.1.
U00096 Genomic DNA. Translation: AAC76486.1.
AP009048 Genomic DNA. Translation: BAE77832.1.
PIRiH65142. RGECH.
RefSeqiNP_417918.1. NC_000913.3.
WP_000130217.1. NZ_LN832404.1.

3D structure databases

ProteinModelPortaliP0AGB3.
SMRiP0AGB3. Positions 35-279.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262497. 257 interactions.
DIPiDIP-46203N.
IntActiP0AGB3. 14 interactions.
STRINGi511145.b3461.

Proteomic databases

PaxDbiP0AGB3.
PRIDEiP0AGB3.

Protocols and materials databases

DNASUi947970.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76486; AAC76486; b3461.
BAE77832; BAE77832; BAE77832.
GeneIDi947970.
KEGGiecj:JW3426.
eco:b3461.
PATRICi32122366. VBIEscCol129921_3560.

Organism-specific databases

EchoBASEiEB0890.
EcoGeneiEG10897. rpoH.

Phylogenomic databases

eggNOGiENOG4105DEK. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270269.
InParanoidiP0AGB3.
KOiK03089.
OMAiLNNDEVH.
PhylomeDBiP0AGB3.

Enzyme and pathway databases

BioCyciEcoCyc:RPOH-MONOMER.
ECOL316407:JW3426-MONOMER.
MetaCyc:RPOH-MONOMER.

Miscellaneous databases

PROiP0AGB3.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
HAMAPiMF_00961. Sigma70_RpoH. 1 hit.
InterProiIPR014284. RNA_pol_sigma-70_dom.
IPR000943. RNA_pol_sigma70.
IPR007627. RNA_pol_sigma70_r2.
IPR007630. RNA_pol_sigma70_r4.
IPR016263. RNA_pol_sigma_factor.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR012759. RNA_pol_sigma_RpoH_proteobac.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04542. Sigma70_r2. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PIRSFiPIRSF000770. RNA_pol_sigma-SigE/K. 1 hit.
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 1 hit.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02392. rpoH_proteo. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPOH_ECOLI
AccessioniPrimary (citable) accession number: P0AGB3
Secondary accession number(s): P00580, Q2M7C4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: December 20, 2005
Last modified: September 7, 2016
This is version 96 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

May only be involved in heat shocks that occur during exponential phase of growth under aerobic conditions. Different mechanisms may play a prime role during stationary phase and anaerobic growth (PubMed:16775749).1 Publication

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. 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.