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Q72L95 (SIGA_THET2) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 70. 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
Synonyms:rpoD
Ordered Locus Names:TT_C0164
OrganismThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) [Complete proteome] [HAMAP]
Taxonomic identifier262724 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

Protein attributes

Sequence length423 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 By similarity. HAMAP-Rule MF_00963

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.3). Ref.3

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.3

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 (Ref.3). Ref.3

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. Ref.3

Sequence similarities

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

Ontologies

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 423423RNA polymerase sigma factor SigA HAMAP-Rule MF_00963
PRO_0000423012

Regions

DNA binding383 – 40220H-T-H motif HAMAP-Rule MF_00963
Region78 – 11336Sigma-70 factor domain-1 HAMAP-Rule MF_00963
Region187 – 25771Sigma-70 factor domain-2 HAMAP-Rule MF_00963
Region266 – 34479Sigma-70 factor domain-3 HAMAP-Rule MF_00963
Region357 – 40953Sigma-70 factor domain-4 HAMAP-Rule MF_00963
Motif211 – 2144Interaction with polymerase core subunit RpoC HAMAP-Rule MF_00963

Secondary structure

..................................................... 423
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q72L95 [UniParc].

Last modified July 5, 2004. Version 1.
Checksum: 931A7B40B92CBC05

FASTA42348,494
        10         20         30         40         50         60 
MKKSKRKNAQ AQEAQETEVL VQEEAEELPE FPEGEPDPDL EDPDLALEDD LLDLPEEGEG 

        70         80         90        100        110        120 
LDLEEEEEDL PIPKISTSDP VRQYLHEIGQ VPLLTLEEEV ELARKVEEGM EAIKKLSEIT 

       130        140        150        160        170        180 
GLDPDLIREV VRAKILGSAR VRHIPGLKET LDPKTVEEID QKLKSLPKEH KRYLHIAREG 

       190        200        210        220        230        240 
EAARQHLIEA NLRLVVSIAK KYTGRGLSFL DLIQEGNQGL IRAVEKFEYK RRFKFSTYAT 

       250        260        270        280        290        300 
WWIRQAINRA IADQARTIRI PVHMVETINK LSRTARQLQQ ELGREPTYEE IAEAMGPGWD 

       310        320        330        340        350        360 
AKRVEETLKI AQEPVSLETP IGDEKDSFYG DFIPDEHLPS PVDAATQSLL SEELEKALSK 

       370        380        390        400        410        420 
LSEREAMVLK LRKGLIDGRE HTLEEVGAFF GVTRERIRQI ENKALRKLKY HESRTRKLRD 


FLD 

« Hide

References

« Hide 'large scale' references
[1]"Cloning and characterization in Escherichia coli of the gene encoding the principal sigma factor of an extreme thermophile, Thermus thermophilus."
Nishiyama M., Kobashi N., Tanaka K., Takahashi H., Tanokura M.
FEMS Microbiol. Lett. 172:179-186(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, GENE NAME.
Strain: HB27 / ATCC BAA-163 / DSM 7039.
[2]"The genome sequence of the extreme thermophile Thermus thermophilus."
Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T., Liesegang H., Johann A., Lienard T., Gohl O., Martinez-Arias R., Jacobi C., Starkuviene V., Schlenczeck S., Dencker S., Huber R., Klenk H.-P., Kramer W., Merkl R., Gottschalk G., Fritz H.-J.
Nat. Biotechnol. 22:547-553(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: HB27 / ATCC BAA-163 / DSM 7039.
[3]"Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution."
Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S.
Nature 417:712-719(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC AND RPOZ, DOMAIN, MOTIF, SUBUNIT.
[4]"Structural basis for transcription regulation by alarmone ppGpp."
Artsimovitch I., Patlan V., Sekine S., Vassylyeva M.N., Hosaka T., Ochi K., Yokoyama S., Vassylyev D.G.
Cell 117:299-310(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC AND RPOZ, SUBUNIT.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB017014 Genomic DNA. Translation: BAA74758.1.
AE017221 Genomic DNA. Translation: AAS80512.1.
RefSeqYP_004139.1. NC_005835.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1IW7X-ray2.60F/P1-423[»]
1SMYX-ray2.70F/P1-423[»]
ProteinModelPortalQ72L95.
SMRQ72L95. Positions 74-423.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING262724.TTC0164.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAS80512; AAS80512; TT_C0164.
GeneID2774849.
KEGGtth:TTC0164.
PATRIC23950721. VBITheThe54392_0165.

Organism-specific databases

CMRSearch...

Phylogenomic databases

eggNOGCOG0568.
KOK03086.
OMALHIAREG.
OrthoDBEOG6XHC70.

Enzyme and pathway databases

BioCycTTHE262724:GCAT-168-MONOMER.

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...

Entry information

Entry nameSIGA_THET2
AccessionPrimary (citable) accession number: Q72L95
Secondary accession number(s): Q9WX78
Entry history
Integrated into UniProtKB/Swiss-Prot: July 24, 2013
Last sequence update: July 5, 2004
Last modified: May 14, 2014
This is version 70 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