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Q9EZJ8

- SIGA_THEAQ

UniProt

Q9EZJ8 - SIGA_THEAQ

Protein

RNA polymerase sigma factor SigA

Gene

sigA

Organism
Thermus aquaticus
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 74 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      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.2 PublicationsUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi398 – 41720H-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

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RNA polymerase sigma factor SigAUniRule annotation
    Gene namesi
    Name:sigAUniRule annotation
    OrganismiThermus aquaticus
    Taxonomic identifieri271 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciThermalesThermaceaeThermus

    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 – 438438RNA polymerase sigma factor SigAPRO_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.5 PublicationsUniRule annotation

    Protein-protein interaction databases

    DIPiDIP-49014N.

    Structurei

    Secondary structure

    1
    438
    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9EZJ8.

    Family & Domainsi

    Region

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

    Motif

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

    Domaini

    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. The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC (PubMed:11931761 and PubMed:22136875).
    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 (PubMed:11931761).1 Publication

    Sequence similaritiesi

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

    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: October 1, 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, 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