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Q72L95

- SIGA_THET2

UniProt

Q72L95 - SIGA_THET2

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Protein

RNA polymerase sigma factor SigA

Gene

sigA

Organism
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
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.UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi383 – 40220H-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

Enzyme and pathway databases

BioCyciTTHE262724:GCAT-168-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor SigAUniRule annotation
Gene namesi
Name:sigAUniRule annotation
Synonyms:rpoD
Ordered Locus Names:TT_C0164
OrganismiThermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Taxonomic identifieri262724 [NCBI]
Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus
ProteomesiUP000000592: Chromosome

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 – 423423RNA polymerase sigma factor SigAPRO_0000423012Add
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 PublicationsUniRule annotation

Protein-protein interaction databases

STRINGi262724.TTC0164.

Structurei

Secondary structure

1
423
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi78 – 9013Combined sources
Helixi97 – 12024Combined sources
Helixi124 – 13613Combined sources
Helixi139 – 1435Combined sources
Beta strandi144 – 1463Combined sources
Beta strandi148 – 1503Combined sources
Helixi154 – 16512Combined sources
Helixi168 – 19023Combined sources
Helixi192 – 1998Combined sources
Helixi203 – 2053Combined sources
Helixi209 – 22618Combined sources
Helixi235 – 25319Combined sources
Beta strandi255 – 2584Combined sources
Helixi262 – 27817Combined sources
Turni279 – 2813Combined sources
Beta strandi282 – 2843Combined sources
Helixi289 – 2957Combined sources
Helixi301 – 31111Combined sources
Beta strandi315 – 3184Combined sources
Turni322 – 3243Combined sources
Beta strandi325 – 3284Combined sources
Helixi329 – 3313Combined sources
Beta strandi336 – 3383Combined sources
Helixi342 – 35918Combined sources
Helixi363 – 37412Combined sources
Helixi385 – 3884Combined sources
Beta strandi389 – 3924Combined sources
Helixi394 – 41421Combined sources
Beta strandi417 – 4204Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1IW7X-ray2.60F/P1-423[»]
1SMYX-ray2.70F/P1-423[»]
ProteinModelPortaliQ72L95.
SMRiQ72L95. Positions 74-423.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni78 – 11336Sigma-70 factor domain-1Add
BLAST
Regioni187 – 25771Sigma-70 factor domain-2Add
BLAST
Regioni266 – 34479Sigma-70 factor domain-3Add
BLAST
Regioni357 – 40953Sigma-70 factor domain-4Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi211 – 2144Interaction with polymerase core subunit RpoC

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:12000971).1 Publication
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 (By similarity). The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC (PubMed:12000971).By similarity1 Publication
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).By similarity

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG0568.
KOiK03086.
OMAiLHIAREG.
OrthoDBiEOG6XHC70.

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.

Q72L95-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MKKSKRKNAQ AQEAQETEVL VQEEAEELPE FPEGEPDPDL EDPDLALEDD
60 70 80 90 100
LLDLPEEGEG LDLEEEEEDL PIPKISTSDP VRQYLHEIGQ VPLLTLEEEV
110 120 130 140 150
ELARKVEEGM EAIKKLSEIT GLDPDLIREV VRAKILGSAR VRHIPGLKET
160 170 180 190 200
LDPKTVEEID QKLKSLPKEH KRYLHIAREG EAARQHLIEA NLRLVVSIAK
210 220 230 240 250
KYTGRGLSFL DLIQEGNQGL IRAVEKFEYK RRFKFSTYAT WWIRQAINRA
260 270 280 290 300
IADQARTIRI PVHMVETINK LSRTARQLQQ ELGREPTYEE IAEAMGPGWD
310 320 330 340 350
AKRVEETLKI AQEPVSLETP IGDEKDSFYG DFIPDEHLPS PVDAATQSLL
360 370 380 390 400
SEELEKALSK LSEREAMVLK LRKGLIDGRE HTLEEVGAFF GVTRERIRQI
410 420
ENKALRKLKY HESRTRKLRD FLD
Length:423
Mass (Da):48,494
Last modified:July 5, 2004 - v1
Checksum:i931A7B40B92CBC05
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB017014 Genomic DNA. Translation: BAA74758.1.
AE017221 Genomic DNA. Translation: AAS80512.1.
RefSeqiYP_004139.1. NC_005835.1.

Genome annotation databases

EnsemblBacteriaiAAS80512; AAS80512; TT_C0164.
GeneIDi2774849.
KEGGitth:TTC0164.
PATRICi23950721. VBITheThe54392_0165.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB017014 Genomic DNA. Translation: BAA74758.1 .
AE017221 Genomic DNA. Translation: AAS80512.1 .
RefSeqi YP_004139.1. NC_005835.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1IW7 X-ray 2.60 F/P 1-423 [» ]
1SMY X-ray 2.70 F/P 1-423 [» ]
ProteinModelPortali Q72L95.
SMRi Q72L95. Positions 74-423.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 262724.TTC0164.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAS80512 ; AAS80512 ; TT_C0164 .
GeneIDi 2774849.
KEGGi tth:TTC0164.
PATRICi 23950721. VBITheThe54392_0165.

Phylogenomic databases

eggNOGi COG0568.
KOi K03086.
OMAi LHIAREG.
OrthoDBi EOG6XHC70.

Enzyme and pathway databases

BioCyci TTHE262724:GCAT-168-MONOMER.

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

« Hide 'large scale' publications
  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. 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. Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC AND RPOZ, SUBUNIT.

Entry informationi

Entry nameiSIGA_THET2
AccessioniPrimary (citable) accession number: Q72L95
Secondary accession number(s): Q9WX78
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 24, 2013
Last sequence update: July 5, 2004
Last modified: November 26, 2014
This is version 74 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, Complete proteome, 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