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Protein

ECF RNA polymerase sigma-E factor

Gene

rpoE

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

Functioni

Sigma factors are initiation factors that promote the attachment of RNA polymerase (RNAP) to specific initiation sites and are then released (PubMed:7889935, PubMed:2691330, PubMed:9159522, PubMed:9159523). Extracytoplasmic function (ECF) sigma-E controls the envelope stress response, responding to periplasmic protein stress, increased levels of periplasmic lipopolysaccharide (LPS) as well as heat shock (PubMed:7889935) and oxidative stress; it controls protein processing in the extracytoplasmic compartment. The 90 member regulon consists of the genes necessary for the synthesis and maintenance of both proteins and LPS of the outer membrane (PubMed:7889934, PubMed:11274153, PubMed:16336047). Indirectly activates transcription of csrB and csrC, 2 sRNAs that antagonize translational regulator CsrA, linking envelope stress, the stringent response and the catabolite repression systems (PubMed:28924029).8 Publications

Activity regulationi

ECF sigma-E is held in an inactive form by its cognate anti-sigma factor (RseA) until released by regulated intramembrane proteolysis (RIP). RIP occurs when an extracytoplasmic signal (periplasmic stress and excess LPS) triggers a concerted proteolytic cascade to transmit information and elicit cellular responses. The anti-sigma factor RseA is an inner membrane protein, binding sigma-E in the cytoplasm and RseB in the periplasm. RseA is first cut extracytoplasmically (site-1 protease, S1P, by DegS), then within the membrane itself (site-2 protease, S2P, by RseP), while cytoplasmic proteases (predominantly ClpX-ClpP) finish degrading the regulatory protein, liberating sigma-E (PubMed:15371343). Degradation of RseA requires 2 signals to activate DegS; an outer membrane protein (OMP) signal activates DegS, while an LPS signal causes release of RseB from RseA, freeing RseA to be cleaved (PubMed:23687042). The rate-limiting step in this protease cascade is the first signal-sensing cleavage (half-life about 1 minute) (PubMed:17210793).4 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi156 – 175H-T-H motifBy similarityAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Sigma factor
Biological processStress response, Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciEcoCyc:RPOE-MONOMER
MetaCyc:RPOE-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
ECF RNA polymerase sigma-E factor
Alternative name(s):
RNA polymerase sigma-E factor
Sigma-24
Gene namesi
Name:rpoE
Synonyms:sigE
Ordered Locus Names:b2573, JW2557
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11897 rpoE

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Reduced viability at 37 degrees Celsius, death at 42 degrees Celsius (PubMed:7889935). Loss of transcription from rpoE-dependent promoters (PubMed:7889935). Increased sensitivity to outer membrane disruption (PubMed:7889934).2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi25L → P in SR1576; loss of sigma factor activity. 1 Publication1
Mutagenesisi165C → A: Binds RNAP and RseA normally. 1 Publication1
Mutagenesisi172S → P in SR1723; loss of sigma factor activity. 1 Publication1
Mutagenesisi178R → G in SR1502; decreased sigma factor activity. Does not bind RseA, still binds RNAP. 2 Publications1
Mutagenesisi181I → A in SR1503; decreased sigma factor activity. Does not bind RseA, still binds RNAP. 1 Publication1
Mutagenesisi185V → A in SR1504; decreased sigma factor activity. Does not bind RseA, still binds RNAP. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000939971 – 191ECF RNA polymerase sigma-E factorAdd BLAST191

Proteomic databases

PaxDbiP0AGB6
PRIDEiP0AGB6

Expressioni

Inductioni

Induced after shifting to 50 degrees Celsius (at protein level) (PubMed:2691330). Induced when the level of outer membrane proteins (OMP) increases (at protein level) (PubMed:8276244, PubMed:10500101). Induced as periplasmic levels of LPS levels increase (PubMed:23687042). Induced by misfolded periplasmic proteins (PubMed:9351822). Transcription positively autoregulated (via promoter P2) (PubMed:7889935). Transcription slightly induced by elevated temperatures (PubMed:7889934). Transiently induced by cold shock in a PNPase-dependent fashion (PubMed:14527658). Translation repressed by CsrA which binds to 3 sites in the 5'-UTR which occludes the ribosome binding site (PubMed:28924029). Translation is coupled to upstream leader peptide RseD, whose stop codon overlaps with the start codon of rpoE; when coupling is eliminated translation is decreased by about 50% (PubMed:28924029). Part of the rseD-rpoE-rseA-rseB-rseC operon (PubMed:9159522, PubMed:9159523, PubMed:28924029).11 Publications

Interactioni

Subunit structurei

Interacts transiently with the RNAP catalytic core formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1 omega subunit) to form the RNAP holoenzyme that can initiate transcription (PubMed:12016219, PubMed:12718891, PubMed:7889935, PubMed:2691330). Interacts 1:1 with anti-sigma-E factor RseA which prevents binding to RNAP catalytic core (PubMed:9159522, PubMed:9159523, PubMed:11777003, PubMed:12016219, PubMed:15371343, PubMed:12718891). An N-terminal (residues 1-108) RseA sigma-E complex also interacts with SspB (PubMed:15371343).8 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
mqsAQ468642EBI-1129580,EBI-1120353

Protein-protein interaction databases

BioGridi4263046, 226 interactors
ComplexPortaliCPX-2532 Sigma-E factor negative regulation complex
DIPiDIP-10774N
IntActiP0AGB6, 30 interactors
STRINGi316385.ECDH10B_2741

Structurei

Secondary structure

1191
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP0AGB6
SMRiP0AGB6
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0AGB6

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1 – 153Binds RNAP core1 PublicationAdd BLAST153
Regioni25 – 92Sigma-70 factor domain-2Add BLAST68
Regioni129 – 180Sigma-70 factor domain-4Add BLAST52

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi48 – 61Polymerase core bindingAdd BLAST14

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.1 Publication
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. Interactions between sigma-70 factor domain-4 and anti-sigma factors prevents interaction of sigma factors with the RNA polymerase catalytic core.2 Publications

Sequence similaritiesi

Belongs to the sigma-70 factor family. ECF subfamily.Curated

Phylogenomic databases

eggNOGiENOG4105EMN Bacteria
COG1595 LUCA
HOGENOMiHOG000094755
InParanoidiP0AGB6
KOiK03088
PhylomeDBiP0AGB6

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR039425 RNA_pol_sigma-70
IPR014284 RNA_pol_sigma-70_dom
IPR000838 RNA_pol_sigma70_ECF_CS
IPR007627 RNA_pol_sigma70_r2
IPR013249 RNA_pol_sigma70_r4_t2
IPR014286 RNA_pol_sigma70_RpoE
IPR013325 RNA_pol_sigma_r2
IPR013324 RNA_pol_sigma_r3/r4-like
IPR036388 WH-like_DNA-bd_sf
PANTHERiPTHR43133 PTHR43133, 1 hit
PfamiView protein in Pfam
PF04542 Sigma70_r2, 1 hit
PF08281 Sigma70_r4_2, 1 hit
SUPFAMiSSF88659 SSF88659, 1 hit
SSF88946 SSF88946, 1 hit
TIGRFAMsiTIGR02939 RpoE_Sigma70, 1 hit
TIGR02937 sigma70-ECF, 1 hit
PROSITEiView protein in PROSITE
PS01063 SIGMA70_ECF, 1 hit

Sequencei

Sequence statusi: Complete.

P0AGB6-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MSEQLTDQVL VERVQKGDQK AFNLLVVRYQ HKVASLVSRY VPSGDVPDVV
60 70 80 90 100
QEAFIKAYRA LDSFRGDSAF YTWLYRIAVN TAKNYLVAQG RRPPSSDVDA
110 120 130 140 150
IEAENFESGG ALKEISNPEN LMLSEELRQI VFRTIESLPE DLRMAITLRE
160 170 180 190
LDGLSYEEIA AIMDCPVGTV RSRIFRAREA IDNKVQPLIR R
Length:191
Mass (Da):21,696
Last modified:December 20, 2005 - v1
Checksum:iC71EEF5939C3611E
GO

Sequence cautioni

The sequence BAA10920 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13169 Genomic DNA No translation available.
U37089 Genomic DNA Translation: AAC45314.1
D64044 Genomic DNA Translation: BAA10920.1 Different initiation.
U00096 Genomic DNA Translation: AAC75626.1
AP009048 Genomic DNA Translation: BAE76749.1
U10148 Genomic DNA Translation: AAA83998.1
PIRiI60227
RefSeqiNP_417068.1, NC_000913.3
WP_001295364.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75626; AAC75626; b2573
BAE76749; BAE76749; BAE76749
GeneIDi947050
KEGGiecj:JW2557
eco:b2573
PATRICifig|1411691.4.peg.4161

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D13169 Genomic DNA No translation available.
U37089 Genomic DNA Translation: AAC45314.1
D64044 Genomic DNA Translation: BAA10920.1 Different initiation.
U00096 Genomic DNA Translation: AAC75626.1
AP009048 Genomic DNA Translation: BAE76749.1
U10148 Genomic DNA Translation: AAA83998.1
PIRiI60227
RefSeqiNP_417068.1, NC_000913.3
WP_001295364.1, NZ_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1OR7X-ray2.00A/B1-191[»]
2H27X-ray2.30A/D122-191[»]
5OR5NMR-A1-64[»]
A79-92[»]
ProteinModelPortaliP0AGB6
SMRiP0AGB6
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263046, 226 interactors
ComplexPortaliCPX-2532 Sigma-E factor negative regulation complex
DIPiDIP-10774N
IntActiP0AGB6, 30 interactors
STRINGi316385.ECDH10B_2741

Proteomic databases

PaxDbiP0AGB6
PRIDEiP0AGB6

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75626; AAC75626; b2573
BAE76749; BAE76749; BAE76749
GeneIDi947050
KEGGiecj:JW2557
eco:b2573
PATRICifig|1411691.4.peg.4161

Organism-specific databases

EchoBASEiEB1843
EcoGeneiEG11897 rpoE

Phylogenomic databases

eggNOGiENOG4105EMN Bacteria
COG1595 LUCA
HOGENOMiHOG000094755
InParanoidiP0AGB6
KOiK03088
PhylomeDBiP0AGB6

Enzyme and pathway databases

BioCyciEcoCyc:RPOE-MONOMER
MetaCyc:RPOE-MONOMER

Miscellaneous databases

EvolutionaryTraceiP0AGB6
PROiPR:P0AGB6

Family and domain databases

Gene3Di1.10.10.10, 1 hit
InterProiView protein in InterPro
IPR039425 RNA_pol_sigma-70
IPR014284 RNA_pol_sigma-70_dom
IPR000838 RNA_pol_sigma70_ECF_CS
IPR007627 RNA_pol_sigma70_r2
IPR013249 RNA_pol_sigma70_r4_t2
IPR014286 RNA_pol_sigma70_RpoE
IPR013325 RNA_pol_sigma_r2
IPR013324 RNA_pol_sigma_r3/r4-like
IPR036388 WH-like_DNA-bd_sf
PANTHERiPTHR43133 PTHR43133, 1 hit
PfamiView protein in Pfam
PF04542 Sigma70_r2, 1 hit
PF08281 Sigma70_r4_2, 1 hit
SUPFAMiSSF88659 SSF88659, 1 hit
SSF88946 SSF88946, 1 hit
TIGRFAMsiTIGR02939 RpoE_Sigma70, 1 hit
TIGR02937 sigma70-ECF, 1 hit
PROSITEiView protein in PROSITE
PS01063 SIGMA70_ECF, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRPOE_ECOLI
AccessioniPrimary (citable) accession number: P0AGB6
Secondary accession number(s): P34086, Q2MAF7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: November 7, 2018
This is version 106 of the entry and version 1 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

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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