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Protein

RNA polymerase sigma factor RpoS

Gene

rpoS

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 to specific initiation sites and are then released. This sigma factor is the master transcriptional regulator of the stationary phase and the general stress response. Controls, positively or negatively, the expression of several hundred genes, which are mainly involved in metabolism, transport, regulation and stress management.UniRule annotation5 Publications
Protects stationary phase cells from killing induced by endoribonuclease MazF.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi288 – 307H-T-H motifUniRule annotationAdd BLAST20

GO - Molecular functioni

  • bacterial-type RNA polymerase core enzyme binding Source: EcoCyc
  • DNA binding Source: UniProtKB-KW
  • DNA binding transcription factor activity Source: InterPro
  • sigma factor activity Source: EcoCyc

GO - Biological processi

  • transcription initiation from bacterial-type RNA polymerase promoter Source: EcoCyc

Keywordsi

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

Enzyme and pathway databases

BioCyciEcoCyc:RPOS-MONOMER
MetaCyc:RPOS-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor RpoSUniRule annotation
Alternative name(s):
Sigma SUniRule annotation
Sigma-38UniRule annotation
Gene namesi
Name:rpoSUniRule annotation
Synonyms:appR, katF, nur, otsX, sigS
Ordered Locus Names:b2741, JW5437
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10510 rpoS

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytoplasm Source: EcoCyc

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Stationary phase cells lose resistance to killing by endoribonuclease MazF.1 Publication

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi173K → E: Eliminates RpoS proteolysis. Lack of interaction with RssB. 1 Publication1
Mutagenesisi174E → T: 2-fold increase in RpoS half-life. Does not affect interaction with RssB. 1 Publication1
Mutagenesisi177V → K: 3-fold increase in RpoS half-life. 1 Publication1
Mutagenesisi178Y → L: Does not affect RpoS half-life. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000939701 – 330RNA polymerase sigma factor RpoSAdd BLAST330

Proteomic databases

EPDiP13445
PaxDbiP13445
PRIDEiP13445

Expressioni

Inductioni

Subject to complex regulation at multiple levels (transcription, translation, regulation of activity and degradation). Transcription is induced during entry into stationary phase and in response to different stresses. Transcription is repressed by antitoxin MqsA (PubMed:21516113). mRNA stability is regulated by small RNA regulators and various proteins such as Hfq, CsdA, CspC and CspE. Finally, the cellular level of RpoS is regulated by proteolysis via RssB and the ClpXP protease.6 Publications

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
rpoBP0A8V25EBI-557581,EBI-544996

GO - Molecular functioni

  • bacterial-type RNA polymerase core enzyme binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4262274, 308 interactors
DIPiDIP-10777N
IntActiP13445, 9 interactors
STRINGi316385.ECDH10B_2909

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5IPLX-ray3.60F1-328[»]
5IPMX-ray4.20F1-328[»]
5IPNX-ray4.61F1-328[»]
ProteinModelPortaliP13445
SMRiP13445
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni56 – 89Sigma-70 factor domain-1Add BLAST34
Regioni94 – 164Sigma-70 factor domain-2Add BLAST71
Regioni174 – 249Sigma-70 factor domain-3Add BLAST76
Regioni262 – 315Sigma-70 factor domain-4Add BLAST54

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi118 – 121Interaction with polymerase core subunit RpoC4

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. RpoS subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DG1 Bacteria
COG0568 LUCA
HOGENOMiHOG000270273
InParanoidiP13445
KOiK03087
OMAiITNRESQ
PhylomeDBiP13445

Family and domain databases

Gene3Di1.10.10.10, 2 hits
HAMAPiMF_00959 Sigma70_RpoS, 1 hit
InterProiView protein in InterPro
IPR014284 RNA_pol_sigma-70_dom
IPR000943 RNA_pol_sigma70
IPR009042 RNA_pol_sigma70_r1_2
IPR007627 RNA_pol_sigma70_r2
IPR007624 RNA_pol_sigma70_r3
IPR007630 RNA_pol_sigma70_r4
IPR013325 RNA_pol_sigma_r2
IPR013324 RNA_pol_sigma_r3/r4-like
IPR012761 RNA_pol_sigma_RpoS
IPR036388 WH-like_DNA-bd_sf
PfamiView protein in Pfam
PF00140 Sigma70_r1_2, 1 hit
PF04542 Sigma70_r2, 1 hit
PF04539 Sigma70_r3, 1 hit
PF04545 Sigma70_r4, 1 hit
PRINTSiPR00046 SIGMA70FCT
SUPFAMiSSF88659 SSF88659, 2 hits
SSF88946 SSF88946, 1 hit
TIGRFAMsiTIGR02394 rpoS_proteo, 1 hit
TIGR02937 sigma70-ECF, 1 hit
PROSITEiView protein in PROSITE
PS00715 SIGMA70_1, 1 hit
PS00716 SIGMA70_2, 1 hit

Sequencei

Sequence statusi: Complete.

P13445-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQNTLKVHD LNEDAEFDEN GVEVFDEKAL VEQEPSDNDL AEEELLSQGA
60 70 80 90 100
TQRVLDATQL YLGEIGYSPL LTAEEEVYFA RRALRGDVAS RRRMIESNLR
110 120 130 140 150
LVVKIARRYG NRGLALLDLI EEGNLGLIRA VEKFDPERGF RFSTYATWWI
160 170 180 190 200
RQTIERAIMN QTRTIRLPIH IVKELNVYLR TARELSHKLD HEPSAEEIAE
210 220 230 240 250
QLDKPVDDVS RMLRLNERIT SVDTPLGGDS EKALLDILAD EKENGPEDTT
260 270 280 290 300
QDDDMKQSIV KWLFELNAKQ REVLARRFGL LGYEAATLED VGREIGLTRE
310 320 330
RVRQIQVEGL RRLREILQTQ GLNIEALFRE
Length:330
Mass (Da):37,972
Last modified:October 1, 1996 - v3
Checksum:i4E6E675E4CA6BC6F
GO

Sequence cautioni

The sequence BAE76818 differs from that shown. Reason: Erroneous termination at position 33. Translated as Gln.Curated
The sequence CAA34435 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
The sequence CAA78692 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25F → L in CAA78692 (PubMed:1437569).Curated1
Sequence conflicti29A → P in CAA34435 (PubMed:2690013).Curated1
Sequence conflicti33Q → L in BAA02747 (PubMed:8475100).Curated1
Sequence conflicti33Q → L in BAA21003 (PubMed:8208244).Curated1
Sequence conflicti196E → V in CAA34435 (PubMed:2690013).Curated1
Sequence conflicti328 – 330FRE → LPRVSKHLSERPVSSEAGFF CAQ in CAA34435 (PubMed:2690013).Curated3

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X16400 Genomic DNA Translation: CAA34435.1 Different initiation.
D13548 Genomic DNA Translation: BAA02747.1
Z14969 Genomic DNA Translation: CAA78692.1 Different initiation.
U29579 Genomic DNA Translation: AAA69251.1
U00096 Genomic DNA Translation: AAC75783.1
AP009048 Genomic DNA Translation: BAE76818.1 Sequence problems.
D17549 Genomic DNA Translation: BAA21003.1
L07869 Unassigned DNA Translation: AAA17876.1
PIRiA65055 RNECKF
RefSeqiNP_417221.1, NC_000913.3
WP_000081586.1, NZ_CP011343.2
WP_000081588.1, NZ_CP014272.1

Genome annotation databases

EnsemblBacteriaiAAC75783; AAC75783; b2741
BAE76818; BAE76818; BAE76818
GeneIDi947210
KEGGiecj:JW5437
eco:b2741
PATRICifig|511145.12.peg.2835

Similar proteinsi

Entry informationi

Entry nameiRPOS_ECOLI
AccessioniPrimary (citable) accession number: P13445
Secondary accession number(s): Q2MA88, Q79EB7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: October 1, 1996
Last modified: June 20, 2018
This is version 168 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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