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

ECF RNA polymerase sigma-E factor

Gene

rpoE

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 (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).7 Publications

Enzyme 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

  • DNA-templated transcription, initiation Source: InterPro
  • regulation of transcription, DNA-templated Source: EcoCyc
  • response to osmotic stress Source: EcoCyc
  • response to temperature stimulus Source: EcoCyc
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:RPOE-MONOMER.
ECOL316407:JW2557-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

  • cytoplasm Source: EcoCyc
Complete GO annotation...

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 (PubMed:2691330) (at protein level), when the level of outer membrane proteins (OMP) increases (PubMed:8276244) (at protein level, PubMed:10500101), as periplasmic levels of LPS levels increase (PubMed:23687042) and by some misfolded periplasmic proteins (PubMed:9351822). Positively autoregulated (via promoter P2) (PubMed:7889935), slightly induced by elevated temperatures (PubMed:7889934). Transiently induced by cold shock in a PNPase-dependent fashion (PubMed:14527658). Part of the rpoE-rseA-rseB-rseC operon (PubMed:9159522, PubMed:9159523).10 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.8 Publications

Binary interactionsi

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

Protein-protein interaction databases

BioGridi4263046. 221 interactors.
DIPiDIP-10774N.
IntActiP0AGB6. 30 interactors.
STRINGi511145.b2573.

Structurei

Secondary structure

1191
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi2 – 15Combined sources14
Helixi19 – 37Combined sources19
Turni38 – 40Combined sources3
Helixi43 – 45Combined sources3
Helixi46 – 60Combined sources15
Helixi61 – 63Combined sources3
Beta strandi66 – 68Combined sources3
Helixi70 – 89Combined sources20
Helixi95 – 104Combined sources10
Beta strandi121 – 123Combined sources3
Helixi124 – 137Combined sources14
Helixi140 – 150Combined sources11
Helixi156 – 162Combined sources7
Helixi167 – 185Combined sources19
Helixi186 – 188Combined sources3

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[»]
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.
OMAiKYQHKVA.
PhylomeDBiP0AGB6.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR014284. 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.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04542. Sigma70_r2. 1 hit.
PF08281. Sigma70_r4_2. 1 hit.
[Graphical view]
SUPFAMiSSF88659. SSF88659. 1 hit.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02939. RpoE_Sigma70. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS01063. SIGMA70_ECF. 1 hit.
[Graphical view]

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.
PATRICi32120545. VBIEscCol129921_2675.

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[»]
ProteinModelPortaliP0AGB6.
SMRiP0AGB6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263046. 221 interactors.
DIPiDIP-10774N.
IntActiP0AGB6. 30 interactors.
STRINGi511145.b2573.

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.
PATRICi32120545. VBIEscCol129921_2675.

Organism-specific databases

EchoBASEiEB1843.
EcoGeneiEG11897. rpoE.

Phylogenomic databases

eggNOGiENOG4105EMN. Bacteria.
COG1595. LUCA.
HOGENOMiHOG000094755.
InParanoidiP0AGB6.
KOiK03088.
OMAiKYQHKVA.
PhylomeDBiP0AGB6.

Enzyme and pathway databases

BioCyciEcoCyc:RPOE-MONOMER.
ECOL316407:JW2557-MONOMER.
MetaCyc:RPOE-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP0AGB6.
PROiP0AGB6.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR014284. 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.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF04542. Sigma70_r2. 1 hit.
PF08281. Sigma70_r4_2. 1 hit.
[Graphical view]
SUPFAMiSSF88659. SSF88659. 1 hit.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02939. RpoE_Sigma70. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS01063. SIGMA70_ECF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPOE_ECOLI
AccessioniPrimary (citable) accession number: P0AGB6
Secondary accession number(s): P34086, Q2MAF7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: November 2, 2016
This is version 93 of the entry and version 1 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.