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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: 4 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 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi398 – 41720H-T-H motif5 Publications
Add
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 SigA
Gene namesi
Name:sigA
OrganismiThermus aquaticus
Taxonomic identifieri271 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Subcellular locationi

Cytoplasm Reviewed prediction UniRule annotation

GO - Cellular componenti

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 438438RNA polymerase sigma factor SigAUniRule annotation
PRO_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.2 Publications

Protein-protein interaction databases

DIPiDIP-49014N.

Structurei

Secondary structure

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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.

Miscellaneous databases

EvolutionaryTraceiQ9EZJ8.

Family & Domainsi

Region

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

Motif

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

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:11931761 and PubMed:12016306).3 Publications
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.3 Publications
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 (1 Publication and 1 Publication).3 Publications
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 (1 Publication).3 Publications

Sequence similaritiesi

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

MKKSKSKKKA AKAQEVEVKE PVKEPEPLPE LEAAEDLQDL PEPDPELLAS    50
EPELEDLADP LDLEGPLEAD LLPEEGLLEE EEEELSLPKV STSDPVRQYL 100
HEIGQVPLLT LEEEIDLARK VEEGMEAIKK LSEATGLDQE LIREVVRAKI 150
LGTARIQKIP GLKEKPDPKT VEEVDGKLKS LPKELKRYLH IAREGEAARQ 200
HLIEANLRLV VSIAKKYTGR GLSFLDLIQE GNQGLIRAVE KFEYKRRFKF 250
STYATWWIRQ AINRAIADQA RTIRIPVHMV ETINKLSRTA RQLQQELGRE 300
PSYEEIAEAM GPGWDAKRVE ETLKIAQEPV SLETPIGDEK DSFYGDFIPD 350
ENLPSPVEAA AQSLLSEELE KALSKLSERE AMVLKLRKGL IDGREHTLEE 400
VGAYFGVTRE RIRQIENKAL RKLKYHESRT RKLRDFLE 438
Length:438
Mass (Da):49,847
Last modified:March 1, 2001 - v1
Checksum:i5D8ACF5713DE55AD
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF291720 Genomic DNA. Translation: AAG36964.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AF291720 Genomic DNA. Translation: AAG36964.1 .

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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: July 9, 2014
This is version 73 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

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