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Q9EZJ8

- SIGA_THEAQ

UniProt

Q9EZJ8 - SIGA_THEAQ

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Protein

RNA polymerase sigma factor SigA

Gene

sigA

Organism
Thermus aquaticus
Status
Reviewed - 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.2 PublicationsUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi398 – 41720H-T-H motifUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-HAMAP
  2. sequence-specific DNA binding transcription factor activity Source: InterPro
  3. sigma factor activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. transcription initiation from bacterial-type RNA polymerase promoter Source: UniProtKB-HAMAP
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

  1. cytoplasm Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 438438RNA polymerase sigma factor SigAPRO_0000423011Add
BLAST

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.5 PublicationsUniRule annotation

Protein-protein interaction databases

DIPiDIP-49014N.

Structurei

Secondary structure

1
438
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi94 – 10310Combined sources
Helixi111 – 13525Combined sources
Helixi139 – 14810Combined sources
Helixi151 – 1533Combined sources
Helixi168 – 17912Combined sources
Helixi183 – 20422Combined sources
Helixi207 – 2148Combined sources
Helixi215 – 2173Combined sources
Beta strandi220 – 2223Combined sources
Helixi224 – 24118Combined sources
Helixi244 – 2463Combined sources
Helixi250 – 26920Combined sources
Helixi277 – 29721Combined sources
Helixi303 – 3108Combined sources
Helixi316 – 3227Combined sources
Helixi323 – 3253Combined sources
Beta strandi326 – 3283Combined sources
Beta strandi370 – 3723Combined sources
Turni373 – 3753Combined sources
Helixi378 – 38710Combined sources
Turni388 – 3925Combined sources
Helixi398 – 4058Combined sources
Helixi409 – 42517Combined sources
Helixi434 – 4374Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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[»]
ProteinModelPortaliQ9EZJ8.
SMRiQ9EZJ8. Positions 89-438.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9EZJ8.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni93 – 12836Sigma-70 factor domain-1Add
BLAST
Regioni202 – 27271Sigma-70 factor domain-2Add
BLAST
Regioni281 – 35979Sigma-70 factor domain-3Add
BLAST
Regioni372 – 42453Sigma-70 factor domain-4Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi226 – 2294Interaction with polymerase core subunit RpoC

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

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA.
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
Entry Method Resolution (Å) Chain Positions PDBsum
1KU2 X-ray 2.90 A/B 92-332 [» ]
1KU3 X-ray 1.80 A 366-438 [» ]
1KU7 X-ray 2.40 A/D 366-438 [» ]
1L9U X-ray 4.00 H/Q 92-438 [» ]
1L9Z X-ray 6.50 H 1-438 [» ]
1RIO X-ray 2.30 H 366-438 [» ]
3LES X-ray 2.77 A/B 93-271 [» ]
3LEV X-ray 2.50 A 93-271 [» ]
3N97 X-ray 3.25 A/D 366-438 [» ]
3UGO X-ray 2.10 A 92-332 [» ]
3UGP X-ray 2.70 A 92-332 [» ]
4KI2 X-ray 3.61 A/B 92-332 [» ]
ProteinModelPortali Q9EZJ8.
SMRi Q9EZJ8. Positions 89-438.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-49014N.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei Q9EZJ8.

Family and domain databases

Gene3Di 1.10.10.10. 2 hits.
HAMAPi MF_00963. Sigma70_RpoD_SigA.
InterProi 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.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR028630. Sigma70_RpoD.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
Pfami PF00140. Sigma70_r1_2. 1 hit.
PF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view ]
PRINTSi PR00046. SIGMA70FCT.
SUPFAMi SSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsi TIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEi PS00716. SIGMA70_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-based analysis of transcription."
    Minakhin L., Nechaev S., Campbell E.A., Severinov K.
    J. Bacteriol. 183:71-76(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  2. "Structure of the bacterial RNA polymerase promoter specificity sigma subunit."
    Campbell E.A., Muzzin O., Chlenov M., Sun J.L., Olson C.A., Weinman O., Trester-Zedlitz M.L., Darst S.A.
    Mol. Cell 9:527-539(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 366-438 IN COMPLEX WITH PROMOTER DNA, PARTIAL PROTEIN SEQUENCE, FUNCTION, DOMAIN, DNA-BINDING, IDENTIFICATION BY MASS SPECTROMETRY.
  3. "Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution."
    Murakami K.S., Masuda S., Darst S.A.
    Science 296:1280-1284(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.00 ANGSTROMS) OF 92-438 IN COMPLEX WITH RPOA; RPOB; RPOC AND RPOZ, DOMAIN, DNA-BINDING, SUBUNIT.
  4. "Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex."
    Murakami K.S., Masuda S., Campbell E.A., Muzzin O., Darst S.A.
    Science 296:1285-1290(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (6.50 ANGSTROMS)IN COMPLEX WITH DNA; RPOA; RPOB; RPOC AND RPOZ, DNA-BINDING, SUBUNIT.
  5. "Structure of a ternary transcription activation complex."
    Jain D., Nickels B.E., Sun L., Hochschild A., Darst S.A.
    Mol. Cell 13:45-53(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 366-438 IN COMPLEX WITH PROMOTER DNA, DNA-BINDING.
  6. "Structural basis for promoter-10 element recognition by the bacterial RNA polymerase sigma subunit."
    Feklistov A., Darst S.A.
    Cell 147:1257-1269(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 92-332 IN COMPLEX WITH PROMOTER DNA, DOMAIN, DNA-BINDING.

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 26, 2014
This is version 76 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

External Data

Dasty 3