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Protein

RNA polymerase sigma factor SigA

Gene

sigA

Organism
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
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 primary sigma factor during exponential growth.UniRule annotation

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi383 – 402H-T-H motifUniRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Sigma factor
Biological processTranscription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor SigAUniRule annotation
Gene namesi
Name:sigAUniRule annotation
Synonyms:rpoD
Ordered Locus Names:TT_C0164
OrganismiThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Taxonomic identifieri262724 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
Proteomesi
  • UP000000592 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004230121 – 423RNA polymerase sigma factor SigAAdd BLAST423

Proteomic databases

PRIDEiQ72L95

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.UniRule annotation2 Publications

Protein-protein interaction databases

STRINGi262724.TTC0164

Structurei

Secondary structure

1423
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi78 – 90Combined sources13
Helixi97 – 120Combined sources24
Helixi124 – 136Combined sources13
Helixi139 – 143Combined sources5
Beta strandi144 – 146Combined sources3
Beta strandi148 – 150Combined sources3
Helixi154 – 165Combined sources12
Helixi168 – 190Combined sources23
Helixi192 – 199Combined sources8
Helixi203 – 205Combined sources3
Helixi209 – 226Combined sources18
Helixi235 – 253Combined sources19
Beta strandi255 – 258Combined sources4
Helixi262 – 278Combined sources17
Turni279 – 281Combined sources3
Beta strandi282 – 284Combined sources3
Helixi289 – 295Combined sources7
Helixi301 – 311Combined sources11
Beta strandi315 – 318Combined sources4
Turni322 – 324Combined sources3
Beta strandi325 – 328Combined sources4
Helixi329 – 331Combined sources3
Beta strandi336 – 338Combined sources3
Helixi342 – 359Combined sources18
Helixi363 – 374Combined sources12
Helixi385 – 388Combined sources4
Beta strandi389 – 392Combined sources4
Helixi394 – 414Combined sources21
Beta strandi417 – 420Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1IW7X-ray2.60F/P1-423[»]
1SMYX-ray2.70F/P1-423[»]
ProteinModelPortaliQ72L95
SMRiQ72L95
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni78 – 113Sigma-70 factor domain-1Add BLAST36
Regioni187 – 257Sigma-70 factor domain-2Add BLAST71
Regioni266 – 344Sigma-70 factor domain-3Add BLAST79
Regioni357 – 409Sigma-70 factor domain-4Add BLAST53

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi211 – 214Interaction with polymerase core subunit RpoC4

Domaini

Contains 4 domains, connected by flexible linkers. In the active conformation, the domains are in an extended conformation, each making extensive interactions with the RNA polymerase catalytic core (PubMed:12000971).1 Publication
In the autoinhibited state, sigma-70 factor domain-1 packs closely together with sigma-70 factor domains-2 and -4, contrary to the extended conformation that is seen when the protein is part of the RNA polymerase holoenzyme.By similarity
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 (By similarity). The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC (PubMed:12000971).By similarity1 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 (By similarity).By similarity

Sequence similaritiesi

Belongs to the sigma-70 factor family. RpoD/SigA subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DG1 Bacteria
COG0568 LUCA
KOiK03086
OMAiTTYLREM

Family and domain databases

Gene3Di1.10.10.10, 2 hits
HAMAPiMF_00963 Sigma70_RpoD_SigA, 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
IPR012760 RNA_pol_sigma_RpoD_C
IPR028630 Sigma70_RpoD
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
TIGRFAMsiTIGR02393 RpoD_Cterm, 1 hit
TIGR02937 sigma70-ECF, 1 hit
PROSITEiView protein in PROSITE
PS00716 SIGMA70_2, 1 hit

Sequencei

Sequence statusi: Complete.

Q72L95-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKSKRKNAQ AQEAQETEVL VQEEAEELPE FPEGEPDPDL EDPDLALEDD
60 70 80 90 100
LLDLPEEGEG LDLEEEEEDL PIPKISTSDP VRQYLHEIGQ VPLLTLEEEV
110 120 130 140 150
ELARKVEEGM EAIKKLSEIT GLDPDLIREV VRAKILGSAR VRHIPGLKET
160 170 180 190 200
LDPKTVEEID QKLKSLPKEH KRYLHIAREG EAARQHLIEA NLRLVVSIAK
210 220 230 240 250
KYTGRGLSFL DLIQEGNQGL IRAVEKFEYK RRFKFSTYAT WWIRQAINRA
260 270 280 290 300
IADQARTIRI PVHMVETINK LSRTARQLQQ ELGREPTYEE IAEAMGPGWD
310 320 330 340 350
AKRVEETLKI AQEPVSLETP IGDEKDSFYG DFIPDEHLPS PVDAATQSLL
360 370 380 390 400
SEELEKALSK LSEREAMVLK LRKGLIDGRE HTLEEVGAFF GVTRERIRQI
410 420
ENKALRKLKY HESRTRKLRD FLD
Length:423
Mass (Da):48,494
Last modified:July 5, 2004 - v1
Checksum:i931A7B40B92CBC05
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB017014 Genomic DNA Translation: BAA74758.1
AE017221 Genomic DNA Translation: AAS80512.1
RefSeqiWP_011172619.1, NC_005835.1

Genome annotation databases

EnsemblBacteriaiAAS80512; AAS80512; TT_C0164
KEGGitth:TT_C0164

Similar proteinsi

Entry informationi

Entry nameiSIGA_THET2
AccessioniPrimary (citable) accession number: Q72L95
Secondary accession number(s): Q9WX78
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 24, 2013
Last sequence update: July 5, 2004
Last modified: April 25, 2018
This is version 91 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
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Main funding by: National Institutes of Health