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Q72L95

- SIGA_THET2

UniProt

Q72L95 - SIGA_THET2

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
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    • History
      Entry version 72 (01 Oct 2014)
      Sequence version 1 (05 Jul 2004)
      Previous versions | rss
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    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

    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-SubCell

    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 – 9013
    Helixi97 – 12024
    Helixi124 – 13613
    Helixi139 – 1435
    Beta strandi144 – 1463
    Beta strandi148 – 1503
    Helixi154 – 16512
    Helixi168 – 19023
    Helixi192 – 1998
    Helixi203 – 2053
    Helixi209 – 22618
    Helixi235 – 25319
    Beta strandi255 – 2584
    Helixi262 – 27817
    Turni279 – 2813
    Beta strandi282 – 2843
    Helixi289 – 2957
    Helixi301 – 31111
    Beta strandi315 – 3184
    Turni322 – 3243
    Beta strandi325 – 3284
    Helixi329 – 3313
    Beta strandi336 – 3383
    Helixi342 – 35918
    Helixi363 – 37412
    Helixi385 – 3884
    Beta strandi389 – 3924
    Helixi394 – 41421
    Beta strandi417 – 4204

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

    MKKSKRKNAQ AQEAQETEVL VQEEAEELPE FPEGEPDPDL EDPDLALEDD    50
    LLDLPEEGEG LDLEEEEEDL PIPKISTSDP VRQYLHEIGQ VPLLTLEEEV 100
    ELARKVEEGM EAIKKLSEIT GLDPDLIREV VRAKILGSAR VRHIPGLKET 150
    LDPKTVEEID QKLKSLPKEH KRYLHIAREG EAARQHLIEA NLRLVVSIAK 200
    KYTGRGLSFL DLIQEGNQGL IRAVEKFEYK RRFKFSTYAT WWIRQAINRA 250
    IADQARTIRI PVHMVETINK LSRTARQLQQ ELGREPTYEE IAEAMGPGWD 300
    AKRVEETLKI AQEPVSLETP IGDEKDSFYG DFIPDEHLPS PVDAATQSLL 350
    SEELEKALSK LSEREAMVLK LRKGLIDGRE HTLEEVGAFF GVTRERIRQI 400
    ENKALRKLKY HESRTRKLRD FLD 423
    Length:423
    Mass (Da):48,494
    Last modified:July 5, 2004 - v1
    Checksum:i931A7B40B92CBC05
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB017014 Genomic DNA. Translation: BAA74758.1.
    AE017221 Genomic DNA. Translation: AAS80512.1.
    RefSeqiWP_011172619.1. NC_005835.1.
    YP_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:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB017014 Genomic DNA. Translation: BAA74758.1 .
    AE017221 Genomic DNA. Translation: AAS80512.1 .
    RefSeqi WP_011172619.1. NC_005835.1.
    YP_004139.1. NC_005835.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

    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: October 1, 2014
    This is version 72 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