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Protein

ECF RNA polymerase sigma factor SigR

Gene

sigR

Organism
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
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. Extracytoplasmic function (ECF) sigma factors are held in an inactive form by an anti-sigma factor (RsrA) until released. Responds to thiol-oxidative stress, involved in regulation of about 30 genes and operons, including the thioredoxin system (trxB-trxA, trxC), ribosomal protein L31, RNA polymerase-binding protein RbpA and mycothiol (MSH) biosynthetic (mshA) and recycling genes (mca). In conjunction with its cognate anti-sigma factor RsrA may sense the intracellular level of reduced MSH.4 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi173 – 19220H-T-H motifBy similarityAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • DNA-templated transcription, initiation Source: InterPro
  • response to oxidative stress Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Sigma factor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
ECF RNA polymerase sigma factor SigR
Short name:
ECF sigma factor SigR
Alternative name(s):
Alternative RNA polymerase sigma factor SigR
RNA polymerase sigma-R factor
Short name:
Sigma-R factor
Gene namesi
Name:sigR
Ordered Locus Names:SCO5216
OrganismiStreptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
Taxonomic identifieri100226 [NCBI]
Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomycesStreptomyces albidoflavus group
Proteomesi
  • UP000001973 Componenti: Chromosome

Pathology & Biotechi

Disruption phenotypei

Increased sensitivity to redox-cycling compounds menadione and plumbagin, and to diamide. Loss of expression of mycothiol biosynthetic and recycling genes.2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 227227ECF RNA polymerase sigma factor SigRPRO_0000423649Add
BLAST

Post-translational modificationi

SigR is present in multiple forms of different pI, suggesting other unknown post-translational modifications.
SigR prime is probably partially degraded by ClpP1-ClpP2.

Proteomic databases

PRIDEiQ7AKG9.

Expressioni

Inductioni

Expressed from 2 promoters, 1 of which (sigRp2) positively regulates its own expression. The same promoter is transiently induced (about 70-fold) by the thiol-oxiding agent diamide. Also induced when mycothiol is oxidized or conjugated.3 Publications

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1 omega subunit) to form the RNA polymerase holoenzyme that can initiate transcription. Interacts with cognate anti-sigma factor RsrA under reducing but not oxiding conditions, which prevents it binding to RNA polymerase. Treatment with the thiol-oxidzing agent diamide inhibits the interaction.4 Publications

Protein-protein interaction databases

STRINGi100226.SCO5216.

Structurei

Secondary structure

1
227
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi29 – 4214Combined sources
Helixi44 – 5512Combined sources
Helixi58 – 7518Combined sources
Helixi76 – 783Combined sources
Beta strandi81 – 833Combined sources
Helixi85 – 9915Combined sources
Helixi148 – 1536Combined sources
Helixi157 – 16711Combined sources
Helixi173 – 1808Combined sources
Helixi184 – 20421Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1H3LX-ray2.38A/B23-109[»]
5FGMX-ray2.60A143-207[»]
ProteinModelPortaliQ7AKG9.
SMRiQ7AKG9. Positions 25-102.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni43 – 10664Sigma-70 factor domain-2Add
BLAST
Regioni148 – 19851Sigma-70 factor domain-4Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi63 – 664Polymerase core bindingSequence analysis

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). Interactions between sigma-70 factor domain-2 and anti-sigma factors prevents interaction of sigma factors with the RNA polymerase catalytic core (Probable).By similarityCurated
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. ECF subfamily.Curated

Phylogenomic databases

eggNOGiENOG4105EMN. Bacteria.
COG1595. LUCA.
HOGENOMiHOG000094755.
InParanoidiQ7AKG9.
KOiK03088.
OMAiQLCDIEG.
OrthoDBiPOG091H04ZH.
PhylomeDBiQ7AKG9.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR014284. RNA_pol_sigma-70_dom.
IPR014293. RNA_pol_sigma70_actinobac.
IPR000838. RNA_pol_sigma70_ECF_CS.
IPR007627. RNA_pol_sigma70_r2.
IPR013249. RNA_pol_sigma70_r4_t2.
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.
TIGRFAMsiTIGR02947. SigH_actino. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS01063. SIGMA70_ECF. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative initiation. AlignAdd to basket

Isoform SigR (identifier: Q7AKG9-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGPVTGTDAG TEHGQAEQPE GRGTGAESTA ERSARFERDA LEFLDQMYSA
60 70 80 90 100
ALRMTRNPAD AEDLVQETYA KAYASFHQFR EGTNLKAWLY RILTNTFINS
110 120 130 140 150
YRKKQREPQR SAAEEIEDWQ LARAESHMST GLRSAESQAL DHLPDSDVKQ
160 170 180 190 200
ALQAIPEEFR IAVYLADVEG FAYKEIADIM GTPIGTVMSR LHRGRRQLRG
210 220
MLEDYARDRG LVPAGAGESN EAKGSGS
Note: Constitutively expressed major isoform, not induced by diamide (at protein level), contributes about half of the diamide-induced expression of the regulon.
Length:227
Mass (Da):25,218
Last modified:May 16, 2012 - v1
Checksum:iAE89C2EF0ED4F366
GO
Isoform SigR prime (identifier: Q7AKG9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MGSAFCPSRSSRADLDWTVLHAAKTAPIRAAGGPDRRLSSDSSETGLGFTTTSEEM

Note: Present in low amounts in unstressed cells, strongly but transiently produced upon diamide induction. Functions as a sigma factor, contributes about half of the diamide-induced expression of the regulon. Unstable, half-life of about 10 minutes.
Show »
Length:282
Mass (Da):30,956
Checksum:i482A1917C58C9858
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 11M → MGSAFCPSRSSRADLDWTVL HAAKTAPIRAAGGPDRRLSS DSSETGLGFTTTSEEM in isoform SigR prime. CuratedVSP_053231

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ010320 Genomic DNA. Translation: CAA09088.1.
AL939122 Genomic DNA. Translation: CAB94601.1.
PIRiT42015.
RefSeqiNP_629363.1. NC_003888.3. [Q7AKG9-1]
WP_003973756.1. NC_003888.3.

Genome annotation databases

EnsemblBacteriaiCAB94601; CAB94601; CAB94601.
GeneIDi1100657.
KEGGisco:SCO5216.
PATRICi23740284. VBIStrCoe124346_5300.

Keywords - Coding sequence diversityi

Alternative initiation

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ010320 Genomic DNA. Translation: CAA09088.1.
AL939122 Genomic DNA. Translation: CAB94601.1.
PIRiT42015.
RefSeqiNP_629363.1. NC_003888.3. [Q7AKG9-1]
WP_003973756.1. NC_003888.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1H3LX-ray2.38A/B23-109[»]
5FGMX-ray2.60A143-207[»]
ProteinModelPortaliQ7AKG9.
SMRiQ7AKG9. Positions 25-102.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi100226.SCO5216.

Proteomic databases

PRIDEiQ7AKG9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB94601; CAB94601; CAB94601.
GeneIDi1100657.
KEGGisco:SCO5216.
PATRICi23740284. VBIStrCoe124346_5300.

Phylogenomic databases

eggNOGiENOG4105EMN. Bacteria.
COG1595. LUCA.
HOGENOMiHOG000094755.
InParanoidiQ7AKG9.
KOiK03088.
OMAiQLCDIEG.
OrthoDBiPOG091H04ZH.
PhylomeDBiQ7AKG9.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
InterProiIPR014284. RNA_pol_sigma-70_dom.
IPR014293. RNA_pol_sigma70_actinobac.
IPR000838. RNA_pol_sigma70_ECF_CS.
IPR007627. RNA_pol_sigma70_r2.
IPR013249. RNA_pol_sigma70_r4_t2.
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.
TIGRFAMsiTIGR02947. SigH_actino. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS01063. SIGMA70_ECF. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSIGR_STRCO
AccessioniPrimary (citable) accession number: Q7AKG9
Secondary accession number(s): O87834
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 16, 2013
Last sequence update: May 16, 2012
Last modified: September 7, 2016
This is version 32 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.