SIGA_THEMA
ID SIGA_THEMA Reviewed; 399 AA.
AC P77994;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 30-MAY-2000, sequence version 3.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=RNA polymerase sigma factor SigA {ECO:0000255|HAMAP-Rule:MF_00963};
DE AltName: Full=Sigma-A;
GN Name=sigA {ECO:0000255|HAMAP-Rule:MF_00963}; Synonyms=rpoD;
GN OrderedLocusNames=TM_1451;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9045836; DOI=10.1128/jb.179.5.1734-1747.1997;
RA Gruber T.M., Bryant D.A.;
RT "Molecular systematic studies of eubacteria, using sigma70-type sigma
RT factors of group 1 and group 2.";
RL J. Bacteriol. 179:1734-1747(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [3]
RP STRUCTURE BY NMR OF 313-399.
RX PubMed=15257291; DOI=10.1038/sj.emboj.7600312;
RA Lambert L.J., Wei Y., Schirf V., Demeler B., Werner M.H.;
RT "T4 AsiA blocks DNA recognition by remodeling sigma70 region 4.";
RL EMBO J. 23:2952-2962(2004).
RN [4]
RP STRUCTURE BY NMR OF 29-95, IDENTIFICATION BY MASS SPECTROMETRY, AND DOMAIN.
RX PubMed=18940669; DOI=10.1016/j.chembiol.2008.09.008;
RA Schwartz E.C., Shekhtman A., Dutta K., Pratt M.R., Cowburn D., Darst S.,
RA Muir T.W.;
RT "A full-length group 1 bacterial sigma factor adopts a compact structure
RT incompatible with DNA binding.";
RL Chem. Biol. 15:1091-1103(2008).
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 {ECO:0000255|HAMAP-Rule:MF_00963}.
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:18940669). {ECO:0000269|PubMed:18940669}.
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:0000269|PubMed:18940669}.
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. The sigma-70 factor domain-2 mediates
CC interaction with the RNA polymerase subunits RpoB and RpoC (By
CC similarity). {ECO:0000250}.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC44889.2; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; U67423; AAC44889.2; ALT_INIT; Genomic_DNA.
DR EMBL; AE000512; AAD36519.1; -; Genomic_DNA.
DR PIR; G72253; G72253.
DR RefSeq; NP_229250.1; NC_000853.1.
DR PDB; 1TTY; NMR; -; A=313-399.
DR PDB; 2K6X; NMR; -; A=29-96.
DR PDBsum; 1TTY; -.
DR PDBsum; 2K6X; -.
DR AlphaFoldDB; P77994; -.
DR SMR; P77994; -.
DR STRING; 243274.THEMA_07060; -.
DR EnsemblBacteria; AAD36519; AAD36519; TM_1451.
DR KEGG; tma:TM1451; -.
DR PATRIC; fig|243274.18.peg.1363; -.
DR eggNOG; COG0568; Bacteria.
DR InParanoid; P77994; -.
DR OMA; YQRWLAE; -.
DR EvolutionaryTrace; P77994; -.
DR Proteomes; UP000008183; 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 Gene3D; 1.10.10.10; -; 2.
DR Gene3D; 1.10.220.120; -; 1.
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; IPR007127; RNA_pol_sigma_70_r1_1.
DR InterPro; IPR042189; RNA_pol_sigma_70_r1_1_sf.
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 Pfam; PF03979; Sigma70_r1_1; 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; SSF88659; SSF88659; 2.
DR SUPFAM; SSF88946; SSF88946; 1.
DR TIGRFAMs; TIGR02393; RpoD_Cterm; 1.
DR TIGRFAMs; TIGR02937; sigma70-ECF; 1.
DR PROSITE; PS00715; SIGMA70_1; 1.
DR PROSITE; PS00716; SIGMA70_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA-binding; Reference proteome; Sigma factor;
KW Transcription; Transcription regulation.
FT CHAIN 1..399
FT /note="RNA polymerase sigma factor SigA"
FT /id="PRO_0000093929"
FT DNA_BIND 353..372
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 1..31
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 30..107
FT /note="Sigma-70 factor domain-1"
FT REGION 159..229
FT /note="Sigma-70 factor domain-2"
FT REGION 238..313
FT /note="Sigma-70 factor domain-3"
FT REGION 327..380
FT /note="Sigma-70 factor domain-4"
FT MOTIF 183..186
FT /note="Interaction with polymerase core subunit RpoC"
FT COMPBIAS 1..26
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 29..45
FT /evidence="ECO:0007829|PDB:2K6X"
FT HELIX 50..56
FT /evidence="ECO:0007829|PDB:2K6X"
FT HELIX 66..77
FT /evidence="ECO:0007829|PDB:2K6X"
FT STRAND 92..94
FT /evidence="ECO:0007829|PDB:2K6X"
FT HELIX 323..328
FT /evidence="ECO:0007829|PDB:1TTY"
FT HELIX 333..343
FT /evidence="ECO:0007829|PDB:1TTY"
FT TURN 344..347
FT /evidence="ECO:0007829|PDB:1TTY"
FT HELIX 353..359
FT /evidence="ECO:0007829|PDB:1TTY"
FT HELIX 364..378
FT /evidence="ECO:0007829|PDB:1TTY"
FT STRAND 382..384
FT /evidence="ECO:0007829|PDB:1TTY"
FT HELIX 385..393
FT /evidence="ECO:0007829|PDB:1TTY"
FT TURN 394..396
FT /evidence="ECO:0007829|PDB:1TTY"
SQ SEQUENCE 399 AA; 46534 MW; BF9B519E8C4890A7 CRC64;
MNEEQQVLQE QHQEQTQEQT QEQKETLPPQ IERRIKKLIS LGKKKGYITY EDIDKAFPPD
FEGFDTNLIE RIHEELEKHG INIVENEPEE EEISASSDEQ ELEELLEKES PEIHDSSNVR
DSIKMYLKEI GKIPLLTPAQ ERELARRAQM GDKKAKEKLI TSNLRLVVSI AKRYMGRGLS
FQDLIQEGNI GLLKAVEKFD WRKGYKFSTY ATWWIRQAIT RAIADQARTI RIPVHMVETI
NKLNRLRREY YQKHGEEPSI EELAKMMGKP PEKIKEILEA AKETISLESP IGEDEDSSIE
DFVADDSIAS PKKEAMRMLM REELEKVLKT LSPREAMVLR MRYGLLDGKP KTLEEVGQYF
NVTRERIRQI EVKALRKLRH PSRSKYLKSL LSLMDENEG
