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Q9EZJ8 (SIGA_THEAQ) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 72. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA polymerase sigma factor SigA
Gene names
Name:sigA
OrganismThermus aquaticus
Taxonomic identifier271 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length438 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.1 Ref.2

Subunit structure

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. Ref.3 Ref.4

Subcellular location

Cytoplasm Potential HAMAP-Rule MF_00963.

Domain

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 (Ref.2 and Ref.3). Ref.2 Ref.3 Ref.6

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. Ref.2 Ref.3 Ref.6

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 (Ref.2 and Ref.6). Ref.2 Ref.3 Ref.6

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 (Ref.2). Ref.2 Ref.3 Ref.6

Sequence similarities

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

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
   LigandDNA-binding
   Molecular functionSigma factor
   Technical term3D-structure
Direct protein sequencing
Gene Ontology (GO)
   Biological_processtranscription initiation from bacterial-type RNA polymerase promoter

Inferred from electronic annotation. Source: UniProtKB-HAMAP

   Cellular_componentcytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: UniProtKB-HAMAP

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: InterPro

sigma factor activity

Inferred from electronic annotation. Source: UniProtKB-HAMAP

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 438438RNA polymerase sigma factor SigA HAMAP-Rule MF_00963
PRO_0000423011

Regions

DNA binding398 – 41720H-T-H motif Ref.2 Ref.3 Ref.4 Ref.5 Ref.6
Region93 – 12836Sigma-70 factor domain-1 HAMAP-Rule MF_00963
Region202 – 27271Sigma-70 factor domain-2 HAMAP-Rule MF_00963
Region281 – 35979Sigma-70 factor domain-3 HAMAP-Rule MF_00963
Region372 – 42453Sigma-70 factor domain-4 HAMAP-Rule MF_00963
Motif226 – 2294Interaction with polymerase core subunit RpoC HAMAP-Rule MF_00963

Secondary structure

............................................ 438
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9EZJ8 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: 5D8ACF5713DE55AD

FASTA43849,847
        10         20         30         40         50         60 
MKKSKSKKKA AKAQEVEVKE PVKEPEPLPE LEAAEDLQDL PEPDPELLAS EPELEDLADP 

        70         80         90        100        110        120 
LDLEGPLEAD LLPEEGLLEE EEEELSLPKV STSDPVRQYL HEIGQVPLLT LEEEIDLARK 

       130        140        150        160        170        180 
VEEGMEAIKK LSEATGLDQE LIREVVRAKI LGTARIQKIP GLKEKPDPKT VEEVDGKLKS 

       190        200        210        220        230        240 
LPKELKRYLH IAREGEAARQ HLIEANLRLV VSIAKKYTGR GLSFLDLIQE GNQGLIRAVE 

       250        260        270        280        290        300 
KFEYKRRFKF STYATWWIRQ AINRAIADQA RTIRIPVHMV ETINKLSRTA RQLQQELGRE 

       310        320        330        340        350        360 
PSYEEIAEAM GPGWDAKRVE ETLKIAQEPV SLETPIGDEK DSFYGDFIPD ENLPSPVEAA 

       370        380        390        400        410        420 
AQSLLSEELE KALSKLSERE AMVLKLRKGL IDGREHTLEE VGAYFGVTRE RIRQIENKAL 

       430 
RKLKYHESRT RKLRDFLE 

« Hide

References

[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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF291720 Genomic DNA. Translation: AAG36964.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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/D366-423[»]
3UGOX-ray2.10A92-332[»]
3UGPX-ray2.70A92-332[»]
4KI2X-ray3.61A/B92-332[»]
ProteinModelPortalQ9EZJ8.
SMRQ9EZJ8. Positions 89-438.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-49014N.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D1.10.10.10. 2 hits.
HAMAPMF_00963. Sigma70_RpoD_SigA.
InterProIPR014284. 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]
PfamPF00140. Sigma70_r1_2. 1 hit.
PF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PRINTSPR00046. SIGMA70FCT.
SUPFAMSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEPS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9EZJ8.

Entry information

Entry nameSIGA_THEAQ
AccessionPrimary (citable) accession number: Q9EZJ8
Entry history
Integrated into UniProtKB/Swiss-Prot: July 24, 2013
Last sequence update: March 1, 2001
Last modified: April 16, 2014
This is version 72 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references