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Protein

RNA polymerase sigma factor SigA

Gene

sigA

Organism
Thermus aquaticus
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 annotation2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi398 – 417H-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
OrganismiThermus aquaticus
Taxonomic identifieri271 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

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_00004230111 – 438RNA polymerase sigma factor SigAAdd BLAST438

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 annotation5 Publications

Protein-protein interaction databases

DIPiDIP-49014N.
STRINGi498848.TaqDRAFT_4448.

Structurei

Secondary structure

1438
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi94 – 103Combined sources10
Helixi111 – 135Combined sources25
Helixi139 – 148Combined sources10
Helixi151 – 153Combined sources3
Helixi168 – 179Combined sources12
Helixi183 – 204Combined sources22
Helixi207 – 214Combined sources8
Helixi215 – 217Combined sources3
Beta strandi220 – 222Combined sources3
Helixi224 – 241Combined sources18
Helixi244 – 246Combined sources3
Helixi250 – 269Combined sources20
Helixi277 – 297Combined sources21
Helixi303 – 310Combined sources8
Helixi316 – 322Combined sources7
Helixi323 – 325Combined sources3
Beta strandi326 – 328Combined sources3
Beta strandi370 – 372Combined sources3
Turni373 – 375Combined sources3
Helixi378 – 387Combined sources10
Turni388 – 392Combined sources5
Helixi398 – 405Combined sources8
Helixi409 – 425Combined sources17
Helixi434 – 437Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KU2X-ray2.90A/B92-332[»]
1KU3X-ray1.80A366-438[»]
1KU7X-ray2.40A/D366-438[»]
1L9UX-ray4.00H/Q92-438[»]
1L9ZX-ray6.50H1-438[»]
1RIOX-ray2.30H366-438[»]
3LESX-ray2.77A/B93-271[»]
3LEVX-ray2.50A93-271[»]
3N97X-ray3.25A/D366-438[»]
3UGOX-ray2.10A92-332[»]
3UGPX-ray2.70A92-332[»]
4KI2X-ray3.61A/B92-332[»]
4XLNX-ray4.00F/L92-438[»]
4XLPX-ray4.00F/L92-438[»]
4XLQX-ray4.60F/L92-438[»]
4XLRX-ray4.30F/L92-438[»]
4XLSX-ray4.01F/L92-438[»]
ProteinModelPortaliQ9EZJ8.
SMRiQ9EZJ8.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9EZJ8.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni93 – 128Sigma-70 factor domain-1Add BLAST36
Regioni202 – 272Sigma-70 factor domain-2Add BLAST71
Regioni281 – 359Sigma-70 factor domain-3Add BLAST79
Regioni372 – 424Sigma-70 factor domain-4Add BLAST53

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi226 – 229Interaction with polymerase core subunit RpoC4

Domaini

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. The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC (PubMed:11931761 and PubMed:22136875).
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 (PubMed:11931761).1 Publication

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.

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.

Q9EZJ8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKKSKSKKKA AKAQEVEVKE PVKEPEPLPE LEAAEDLQDL PEPDPELLAS
60 70 80 90 100
EPELEDLADP LDLEGPLEAD LLPEEGLLEE EEEELSLPKV STSDPVRQYL
110 120 130 140 150
HEIGQVPLLT LEEEIDLARK VEEGMEAIKK LSEATGLDQE LIREVVRAKI
160 170 180 190 200
LGTARIQKIP GLKEKPDPKT VEEVDGKLKS LPKELKRYLH IAREGEAARQ
210 220 230 240 250
HLIEANLRLV VSIAKKYTGR GLSFLDLIQE GNQGLIRAVE KFEYKRRFKF
260 270 280 290 300
STYATWWIRQ AINRAIADQA RTIRIPVHMV ETINKLSRTA RQLQQELGRE
310 320 330 340 350
PSYEEIAEAM GPGWDAKRVE ETLKIAQEPV SLETPIGDEK DSFYGDFIPD
360 370 380 390 400
ENLPSPVEAA AQSLLSEELE KALSKLSERE AMVLKLRKGL IDGREHTLEE
410 420 430
VGAYFGVTRE RIRQIENKAL RKLKYHESRT RKLRDFLE
Length:438
Mass (Da):49,847
Last modified:March 1, 2001 - v1
Checksum:i5D8ACF5713DE55AD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF291720 Genomic DNA. Translation: AAG36964.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF291720 Genomic DNA. Translation: AAG36964.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1KU2X-ray2.90A/B92-332[»]
1KU3X-ray1.80A366-438[»]
1KU7X-ray2.40A/D366-438[»]
1L9UX-ray4.00H/Q92-438[»]
1L9ZX-ray6.50H1-438[»]
1RIOX-ray2.30H366-438[»]
3LESX-ray2.77A/B93-271[»]
3LEVX-ray2.50A93-271[»]
3N97X-ray3.25A/D366-438[»]
3UGOX-ray2.10A92-332[»]
3UGPX-ray2.70A92-332[»]
4KI2X-ray3.61A/B92-332[»]
4XLNX-ray4.00F/L92-438[»]
4XLPX-ray4.00F/L92-438[»]
4XLQX-ray4.60F/L92-438[»]
4XLRX-ray4.30F/L92-438[»]
4XLSX-ray4.01F/L92-438[»]
ProteinModelPortaliQ9EZJ8.
SMRiQ9EZJ8.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-49014N.
STRINGi498848.TaqDRAFT_4448.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.

Miscellaneous databases

EvolutionaryTraceiQ9EZJ8.

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_THEAQ
AccessioniPrimary (citable) accession number: Q9EZJ8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 24, 2013
Last sequence update: March 1, 2001
Last modified: November 2, 2016
This is version 83 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, 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.