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Protein

RNA polymerase sigma factor RpoS

Gene

rpoS

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 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)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi288 – 30720H-T-H motifUniRule annotationAdd
BLAST

GO - Molecular functioni

  • bacterial-type RNA polymerase core enzyme binding Source: EcoCyc
  • DNA binding Source: UniProtKB-HAMAP
  • sigma factor activity Source: EcoCyc
  • transcription factor activity, sequence-specific DNA binding Source: InterPro

GO - Biological processi

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:RPOS-MONOMER.
ECOL316407:JW5437-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10510. rpoS.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytoplasm Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

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

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi173 – 1731K → E: Eliminates RpoS proteolysis. Lack of interaction with RssB. 1 Publication
Mutagenesisi174 – 1741E → T: 2-fold increase in RpoS half-life. Does not affect interaction with RssB. 1 Publication
Mutagenesisi177 – 1771V → K: 3-fold increase in RpoS half-life. 1 Publication
Mutagenesisi178 – 1781Y → L: Does not affect RpoS half-life. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 330330RNA polymerase sigma factor RpoSPRO_0000093970Add
BLAST

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

GO - Molecular functioni

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

Protein-protein interaction databases

BioGridi4262274. 303 interactions.
DIPiDIP-10777N.
IntActiP13445. 9 interactions.
MINTiMINT-1228474.
STRINGi511145.b2741.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5IPLX-ray3.60F1-328[»]
5IPMX-ray4.20F1-328[»]
5IPNX-ray4.61F1-328[»]
ProteinModelPortaliP13445.
SMRiP13445. Positions 41-314.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni56 – 8934Sigma-70 factor domain-1Add
BLAST
Regioni94 – 16471Sigma-70 factor domain-2Add
BLAST
Regioni174 – 24976Sigma-70 factor domain-3Add
BLAST
Regioni262 – 31554Sigma-70 factor domain-4Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi118 – 1214Interaction 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. RpoS subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270273.
InParanoidiP13445.
KOiK03087.
OMAiKYIDYTR.
PhylomeDBiP13445.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00959. Sigma70_RpoS. 1 hit.
InterProiIPR014284. 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.
IPR012761. RNA_pol_sigma_RpoS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00140. Sigma70_r1_2. 1 hit.
PF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02394. rpoS_proteo. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]

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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti25 – 251F → L in CAA78692 (PubMed:1437569).Curated
Sequence conflicti29 – 291A → P in CAA34435 (PubMed:2690013).Curated
Sequence conflicti33 – 331Q → L in BAA02747 (PubMed:8475100).Curated
Sequence conflicti33 – 331Q → L in BAA21003 (PubMed:8208244).Curated
Sequence conflicti196 – 1961E → V in CAA34435 (PubMed:2690013).Curated
Sequence conflicti328 – 3303FRE → LPRVSKHLSERPVSSEAGFF CAQ in CAA34435 (PubMed:2690013).Curated

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_000081588.1. NZ_CP014272.1.

Genome annotation databases

EnsemblBacteriaiAAC75783; AAC75783; b2741.
BAE76818; BAE76818; BAE76818.
GeneIDi947210.
KEGGiecj:JW5437.
eco:b2741.
PATRICi32120886. VBIEscCol129921_2835.

Cross-referencesi

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_000081588.1. NZ_CP014272.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
5IPLX-ray3.60F1-328[»]
5IPMX-ray4.20F1-328[»]
5IPNX-ray4.61F1-328[»]
ProteinModelPortaliP13445.
SMRiP13445. Positions 41-314.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262274. 303 interactions.
DIPiDIP-10777N.
IntActiP13445. 9 interactions.
MINTiMINT-1228474.
STRINGi511145.b2741.

Proteomic databases

EPDiP13445.
PaxDbiP13445.
PRIDEiP13445.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75783; AAC75783; b2741.
BAE76818; BAE76818; BAE76818.
GeneIDi947210.
KEGGiecj:JW5437.
eco:b2741.
PATRICi32120886. VBIEscCol129921_2835.

Organism-specific databases

EchoBASEiEB0505.
EcoGeneiEG10510. rpoS.

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270273.
InParanoidiP13445.
KOiK03087.
OMAiKYIDYTR.
PhylomeDBiP13445.

Enzyme and pathway databases

BioCyciEcoCyc:RPOS-MONOMER.
ECOL316407:JW5437-MONOMER.
MetaCyc:RPOS-MONOMER.

Miscellaneous databases

PROiP13445.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00959. Sigma70_RpoS. 1 hit.
InterProiIPR014284. 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.
IPR012761. RNA_pol_sigma_RpoS.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF00140. Sigma70_r1_2. 1 hit.
PF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02394. rpoS_proteo. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPOS_ECOLI
AccessioniPrimary (citable) accession number: P13445
Secondary accession number(s): Q2MA88, Q79EB7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1990
Last sequence update: October 1, 1996
Last modified: September 7, 2016
This is version 154 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, 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.