ID SIGA_THEAQ Reviewed; 438 AA. AC Q9EZJ8; DT 24-JUL-2013, integrated into UniProtKB/Swiss-Prot. DT 01-MAR-2001, sequence version 1. DT 27-MAR-2024, entry version 112. DE RecName: Full=RNA polymerase sigma factor SigA {ECO:0000255|HAMAP-Rule:MF_00963}; GN Name=sigA {ECO:0000255|HAMAP-Rule:MF_00963}; OS Thermus aquaticus. OC Bacteria; Deinococcota; Deinococci; Thermales; Thermaceae; Thermus. OX NCBI_TaxID=271; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION. RX PubMed=11114902; DOI=10.1128/jb.183.1.71-76.2001; RA Minakhin L., Nechaev S., Campbell E.A., Severinov K.; RT "Recombinant Thermus aquaticus RNA polymerase, a new tool for structure- RT based analysis of transcription."; RL J. Bacteriol. 183:71-76(2001). RN [2] RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 366-438 IN COMPLEX WITH PROMOTER RP DNA, PARTIAL PROTEIN SEQUENCE, FUNCTION, DOMAIN, DNA-BINDING, AND RP IDENTIFICATION BY MASS SPECTROMETRY. RX PubMed=11931761; DOI=10.1016/s1097-2765(02)00470-7; RA Campbell E.A., Muzzin O., Chlenov M., Sun J.L., Olson C.A., Weinman O., RA Trester-Zedlitz M.L., Darst S.A.; RT "Structure of the bacterial RNA polymerase promoter specificity sigma RT subunit."; RL Mol. Cell 9:527-539(2002). RN [3] RP X-RAY CRYSTALLOGRAPHY (4.00 ANGSTROMS) OF 92-438 IN COMPLEX WITH RPOA; RP RPOB; RPOC AND RPOZ, DOMAIN, DNA-BINDING, AND SUBUNIT. RX PubMed=12016306; DOI=10.1126/science.1069594; RA Murakami K.S., Masuda S., Darst S.A.; RT "Structural basis of transcription initiation: RNA polymerase holoenzyme at RT 4 A resolution."; RL Science 296:1280-1284(2002). RN [4] RP X-RAY CRYSTALLOGRAPHY (6.50 ANGSTROMS)IN COMPLEX WITH DNA; RPOA; RPOB; RPOC RP AND RPOZ, DNA-BINDING, AND SUBUNIT. RX PubMed=12016307; DOI=10.1126/science.1069595; RA Murakami K.S., Masuda S., Campbell E.A., Muzzin O., Darst S.A.; RT "Structural basis of transcription initiation: an RNA polymerase RT holoenzyme-DNA complex."; RL Science 296:1285-1290(2002). RN [5] RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 366-438 IN COMPLEX WITH PROMOTER RP DNA, AND DNA-BINDING. RX PubMed=14731393; DOI=10.1016/s1097-2765(03)00483-0; RA Jain D., Nickels B.E., Sun L., Hochschild A., Darst S.A.; RT "Structure of a ternary transcription activation complex."; RL Mol. Cell 13:45-53(2004). RN [6] RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 92-332 IN COMPLEX WITH PROMOTER RP DNA, DOMAIN, AND DNA-BINDING. RX PubMed=22136875; DOI=10.1016/j.cell.2011.10.041; RA Feklistov A., Darst S.A.; RT "Structural basis for promoter-10 element recognition by the bacterial RNA RT polymerase sigma subunit."; RL Cell 147:1257-1269(2011). 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 ECO:0000269|PubMed:11114902, ECO:0000269|PubMed:11931761}. 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:11931761, ECO:0000269|PubMed:12016306, CC ECO:0000269|PubMed:12016307, ECO:0000269|PubMed:14731393, CC ECO:0000269|PubMed:22136875}. 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:11931761, PubMed:12016306). 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. The sigma-70 factor domain-2 mediates CC interaction with the RNA polymerase subunits RpoB and RpoC CC (PubMed:11931761, PubMed:22136875). 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 (PubMed:11931761). CC {ECO:0000269|PubMed:11931761}. CC -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA subfamily. CC {ECO:0000255|HAMAP-Rule:MF_00963}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; AF291720; AAG36964.1; -; Genomic_DNA. DR PDB; 1KU2; X-ray; 2.90 A; A/B=92-332. DR PDB; 1KU3; X-ray; 1.80 A; A=366-438. DR PDB; 1KU7; X-ray; 2.40 A; A/D=366-438. DR PDB; 1L9U; X-ray; 4.00 A; H/Q=92-438. DR PDB; 1L9Z; X-ray; 6.50 A; H=1-438. DR PDB; 1RIO; X-ray; 2.30 A; H=366-438. DR PDB; 3LES; X-ray; 2.77 A; A/B=93-271. DR PDB; 3LEV; X-ray; 2.50 A; A=93-271. DR PDB; 3N97; X-ray; 3.25 A; A/D=366-438. DR PDB; 3UGO; X-ray; 2.10 A; A=92-332. DR PDB; 3UGP; X-ray; 2.70 A; A=92-332. DR PDB; 4KI2; X-ray; 3.61 A; A/B=92-332. DR PDB; 4XLN; X-ray; 4.00 A; F/L=92-438. DR PDB; 4XLP; X-ray; 4.00 A; F/L=92-438. DR PDB; 4XLQ; X-ray; 4.60 A; F/L=92-438. DR PDB; 4XLR; X-ray; 4.30 A; F/L=92-438. DR PDB; 4XLS; X-ray; 4.01 A; F/L=92-438. DR PDB; 5TJG; X-ray; 2.60 A; F=92-438. DR PDBsum; 1KU2; -. DR PDBsum; 1KU3; -. DR PDBsum; 1KU7; -. DR PDBsum; 1L9U; -. DR PDBsum; 1L9Z; -. DR PDBsum; 1RIO; -. DR PDBsum; 3LES; -. DR PDBsum; 3LEV; -. DR PDBsum; 3N97; -. DR PDBsum; 3UGO; -. DR PDBsum; 3UGP; -. DR PDBsum; 4KI2; -. DR PDBsum; 4XLN; -. DR PDBsum; 4XLP; -. DR PDBsum; 4XLQ; -. DR PDBsum; 4XLR; -. DR PDBsum; 4XLS; -. DR PDBsum; 5TJG; -. DR AlphaFoldDB; Q9EZJ8; -. DR SMR; Q9EZJ8; -. DR DIP; DIP-49014N; -. DR IntAct; Q9EZJ8; 1. DR EvolutionaryTrace; Q9EZJ8; -. 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; IDA:CACAO. 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..438 FT /note="RNA polymerase sigma factor SigA" FT /id="PRO_0000423011" FT DNA_BIND 398..417 FT /note="H-T-H motif" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963" FT REGION 1..69 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT REGION 93..128 FT /note="Sigma-70 factor domain-1" FT REGION 202..272 FT /note="Sigma-70 factor domain-2" FT REGION 281..359 FT /note="Sigma-70 factor domain-3" FT REGION 372..424 FT /note="Sigma-70 factor domain-4" FT MOTIF 226..229 FT /note="Interaction with polymerase core subunit RpoC" FT COMPBIAS 10..30 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 31..63 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT HELIX 94..103 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 111..135 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 139..148 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 151..153 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 168..179 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 183..204 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 207..214 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 215..217 FT /evidence="ECO:0007829|PDB:3UGO" FT STRAND 220..222 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 224..241 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 244..246 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 250..269 FT /evidence="ECO:0007829|PDB:3UGO" FT HELIX 277..297 FT /evidence="ECO:0007829|PDB:5TJG" FT HELIX 303..310 FT /evidence="ECO:0007829|PDB:5TJG" FT HELIX 316..326 FT /evidence="ECO:0007829|PDB:5TJG" FT HELIX 344..346 FT /evidence="ECO:0007829|PDB:5TJG" FT STRAND 351..353 FT /evidence="ECO:0007829|PDB:5TJG" FT STRAND 370..372 FT /evidence="ECO:0007829|PDB:1KU3" FT TURN 373..375 FT /evidence="ECO:0007829|PDB:1KU3" FT HELIX 378..387 FT /evidence="ECO:0007829|PDB:1KU3" FT TURN 388..392 FT /evidence="ECO:0007829|PDB:1KU3" FT HELIX 398..405 FT /evidence="ECO:0007829|PDB:1KU3" FT HELIX 409..425 FT /evidence="ECO:0007829|PDB:1KU3" FT HELIX 434..437 FT /evidence="ECO:0007829|PDB:1KU7" SQ SEQUENCE 438 AA; 49847 MW; 5D8ACF5713DE55AD CRC64; MKKSKSKKKA AKAQEVEVKE PVKEPEPLPE LEAAEDLQDL PEPDPELLAS EPELEDLADP LDLEGPLEAD LLPEEGLLEE EEEELSLPKV STSDPVRQYL HEIGQVPLLT LEEEIDLARK VEEGMEAIKK LSEATGLDQE LIREVVRAKI LGTARIQKIP GLKEKPDPKT VEEVDGKLKS LPKELKRYLH IAREGEAARQ HLIEANLRLV VSIAKKYTGR GLSFLDLIQE GNQGLIRAVE KFEYKRRFKF STYATWWIRQ AINRAIADQA RTIRIPVHMV ETINKLSRTA RQLQQELGRE PSYEEIAEAM GPGWDAKRVE ETLKIAQEPV SLETPIGDEK DSFYGDFIPD ENLPSPVEAA AQSLLSEELE KALSKLSERE AMVLKLRKGL IDGREHTLEE VGAYFGVTRE RIRQIENKAL RKLKYHESRT RKLRDFLE //