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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: Annotation score: 3 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 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

Complete GO annotation...

Keywords - Molecular functioni

Sigma factor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

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

Complete GO annotation...

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.
OMAiLHIAREG.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 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.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR028630. Sigma70_RpoD.
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.
TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00716. SIGMA70_2. 1 hit.
[Graphical view]

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.
PATRICi23950721. VBITheThe54392_0165.

Cross-referencesi

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.

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...

Protein-protein interaction databases

STRINGi262724.TTC0164.

Proteomic databases

PRIDEiQ72L95.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS80512; AAS80512; TT_C0164.
KEGGitth:TT_C0164.
PATRICi23950721. VBITheThe54392_0165.

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
KOiK03086.
OMAiLHIAREG.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 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.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR028630. Sigma70_RpoD.
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.
TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSIGA_THET2
AccessioniPrimary (citable) accession number: Q72L95
Secondary accession number(s): Q9WX78
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 24, 2013
Last sequence update: July 5, 2004
Last modified: November 2, 2016
This is version 84 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

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.