ID SIGA_THET2 Reviewed; 423 AA.
AC Q72L95; Q9WX78;
DT 24-JUL-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 27-MAR-2024, entry version 116.
DE RecName: Full=RNA polymerase sigma factor SigA {ECO:0000255|HAMAP-Rule:MF_00963};
GN Name=sigA {ECO:0000255|HAMAP-Rule:MF_00963}; Synonyms=rpoD;
GN OrderedLocusNames=TT_C0164;
OS Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27).
OC Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=262724;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10, AND GENE NAME.
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=10188247; DOI=10.1111/j.1574-6968.1999.tb13467.x;
RA Nishiyama M., Kobashi N., Tanaka K., Takahashi H., Tanokura M.;
RT "Cloning and characterization in Escherichia coli of the gene encoding the
RT principal sigma factor of an extreme thermophile, Thermus thermophilus.";
RL FEMS Microbiol. Lett. 172:179-186(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-163 / DSM 7039 / HB27;
RX PubMed=15064768; DOI=10.1038/nbt956;
RA Henne A., Brueggemann H., Raasch C., Wiezer A., Hartsch T., Liesegang H.,
RA Johann A., Lienard T., Gohl O., Martinez-Arias R., Jacobi C.,
RA Starkuviene V., Schlenczeck S., Dencker S., Huber R., Klenk H.-P.,
RA Kramer W., Merkl R., Gottschalk G., Fritz H.-J.;
RT "The genome sequence of the extreme thermophile Thermus thermophilus.";
RL Nat. Biotechnol. 22:547-553(2004).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC AND
RP RPOZ, DOMAIN, MOTIF, AND SUBUNIT.
RX PubMed=12000971; DOI=10.1038/nature752;
RA Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N.,
RA Borukhov S., Yokoyama S.;
RT "Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A
RT resolution.";
RL Nature 417:712-719(2002).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC AND
RP RPOZ, AND SUBUNIT.
RX PubMed=15109491; DOI=10.1016/s0092-8674(04)00401-5;
RA Artsimovitch I., Patlan V., Sekine S., Vassylyeva M.N., Hosaka T., Ochi K.,
RA Yokoyama S., Vassylyev D.G.;
RT "Structural basis for transcription regulation by alarmone ppGpp.";
RL Cell 117:299-310(2004).
CC -!- FUNCTION: Sigma factors are initiation factors that promote the
CC attachment of RNA polymerase to specific initiation sites and are then
CC released. This sigma factor is the primary sigma factor during
CC exponential growth. {ECO:0000255|HAMAP-Rule:MF_00963}.
CC -!- SUBUNIT: Interacts transiently with the RNA polymerase catalytic core
CC formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1
CC omega subunit) to form the RNA polymerase holoenzyme that can initiate
CC transcription. {ECO:0000255|HAMAP-Rule:MF_00963,
CC ECO:0000269|PubMed:12000971, ECO:0000269|PubMed:15109491}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00963}.
CC -!- DOMAIN: Contains 4 domains, connected by flexible linkers. In the
CC active conformation, the domains are in an extended conformation, each
CC making extensive interactions with the RNA polymerase catalytic core
CC (PubMed:12000971). {ECO:0000269|PubMed:12000971}.
CC -!- DOMAIN: In the autoinhibited state, sigma-70 factor domain-1 packs
CC closely together with sigma-70 factor domains-2 and -4, contrary to the
CC extended conformation that is seen when the protein is part of the RNA
CC polymerase holoenzyme. {ECO:0000250}.
CC -!- DOMAIN: The sigma-70 factor domain-2 mediates sequence-specific
CC interaction with the -10 element in promoter DNA, and plays an
CC important role in melting the double-stranded DNA and the formation of
CC the transcription bubble (By similarity). The sigma-70 factor domain-2
CC mediates interaction with the RNA polymerase subunits RpoB and RpoC
CC (PubMed:12000971). {ECO:0000250, ECO:0000269|PubMed:12000971}.
CC -!- DOMAIN: The sigma-70 factor domain-4 contains a helix-turn-helix (H-T-
CC H) motif that mediates interaction with the -35 element in promoter
CC DNA. The domain also mediates interaction with the RNA polymerase
CC subunit RpoA. Interactions between sigma-70 factor domain-4 and anti-
CC sigma factors prevents interaction of sigma factors with the RNA
CC polymerase catalytic core (By similarity). {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00963}.
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DR EMBL; AB017014; BAA74758.1; -; Genomic_DNA.
DR EMBL; AE017221; AAS80512.1; -; Genomic_DNA.
DR RefSeq; WP_011172619.1; NZ_CP133179.1.
DR PDB; 1IW7; X-ray; 2.60 A; F/P=1-423.
DR PDB; 1SMY; X-ray; 2.70 A; F/P=1-423.
DR PDBsum; 1IW7; -.
DR PDBsum; 1SMY; -.
DR AlphaFoldDB; Q72L95; -.
DR SMR; Q72L95; -.
DR KEGG; tth:TT_C0164; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_3_3_0; -.
DR OrthoDB; 9809557at2; -.
DR Proteomes; UP000000592; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016987; F:sigma factor activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006352; P:DNA-templated transcription initiation; IEA:UniProtKB-UniRule.
DR CDD; cd06171; Sigma70_r4; 1.
DR Gene3D; 1.20.120.1810; -; 1.
DR Gene3D; 1.10.10.10; Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain; 2.
DR HAMAP; MF_00963; Sigma70_RpoD_SigA; 1.
DR InterPro; IPR014284; RNA_pol_sigma-70_dom.
DR InterPro; IPR000943; RNA_pol_sigma70.
DR InterPro; IPR009042; RNA_pol_sigma70_r1_2.
DR InterPro; IPR007627; RNA_pol_sigma70_r2.
DR InterPro; IPR007624; RNA_pol_sigma70_r3.
DR InterPro; IPR007630; RNA_pol_sigma70_r4.
DR InterPro; IPR013325; RNA_pol_sigma_r2.
DR InterPro; IPR013324; RNA_pol_sigma_r3/r4-like.
DR InterPro; IPR012760; RNA_pol_sigma_RpoD_C.
DR InterPro; IPR028630; Sigma70_RpoD.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR NCBIfam; TIGR02393; RpoD_Cterm; 1.
DR NCBIfam; TIGR02937; sigma70-ECF; 1.
DR PANTHER; PTHR30603; RNA POLYMERASE SIGMA FACTOR RPO; 1.
DR PANTHER; PTHR30603:SF47; RNA POLYMERASE SIGMA FACTOR SIGF, CHLOROPLASTIC; 1.
DR Pfam; PF00140; Sigma70_r1_2; 1.
DR Pfam; PF04542; Sigma70_r2; 1.
DR Pfam; PF04539; Sigma70_r3; 1.
DR Pfam; PF04545; Sigma70_r4; 1.
DR PRINTS; PR00046; SIGMA70FCT.
DR SUPFAM; SSF88946; Sigma2 domain of RNA polymerase sigma factors; 1.
DR SUPFAM; SSF88659; Sigma3 and sigma4 domains of RNA polymerase sigma factors; 2.
DR PROSITE; PS00716; SIGMA70_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; DNA-binding;
KW Sigma factor; Transcription; Transcription regulation.
FT CHAIN 1..423
FT /note="RNA polymerase sigma factor SigA"
FT /id="PRO_0000423012"
FT DNA_BIND 383..402
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 1..76
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 78..113
FT /note="Sigma-70 factor domain-1"
FT REGION 187..257
FT /note="Sigma-70 factor domain-2"
FT REGION 266..344
FT /note="Sigma-70 factor domain-3"
FT REGION 357..409
FT /note="Sigma-70 factor domain-4"
FT MOTIF 211..214
FT /note="Interaction with polymerase core subunit RpoC"
FT COMPBIAS 19..69
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 78..90
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 97..120
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 124..136
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 139..143
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 144..146
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 148..150
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 154..165
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 168..190
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 192..199
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 209..226
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 235..253
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 255..258
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 262..278
FT /evidence="ECO:0007829|PDB:1IW7"
FT TURN 279..281
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 282..284
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 289..295
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 301..311
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 315..318
FT /evidence="ECO:0007829|PDB:1IW7"
FT TURN 322..324
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 325..328
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 329..331
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 342..359
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 363..374
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 385..388
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 389..392
FT /evidence="ECO:0007829|PDB:1IW7"
FT HELIX 394..414
FT /evidence="ECO:0007829|PDB:1IW7"
FT STRAND 417..420
FT /evidence="ECO:0007829|PDB:1SMY"
SQ SEQUENCE 423 AA; 48494 MW; 931A7B40B92CBC05 CRC64;
MKKSKRKNAQ AQEAQETEVL VQEEAEELPE FPEGEPDPDL EDPDLALEDD LLDLPEEGEG
LDLEEEEEDL PIPKISTSDP VRQYLHEIGQ VPLLTLEEEV ELARKVEEGM EAIKKLSEIT
GLDPDLIREV VRAKILGSAR VRHIPGLKET LDPKTVEEID QKLKSLPKEH KRYLHIAREG
EAARQHLIEA NLRLVVSIAK KYTGRGLSFL DLIQEGNQGL IRAVEKFEYK RRFKFSTYAT
WWIRQAINRA IADQARTIRI PVHMVETINK LSRTARQLQQ ELGREPTYEE IAEAMGPGWD
AKRVEETLKI AQEPVSLETP IGDEKDSFYG DFIPDEHLPS PVDAATQSLL SEELEKALSK
LSEREAMVLK LRKGLIDGRE HTLEEVGAFF GVTRERIRQI ENKALRKLKY HESRTRKLRD
FLD
//
