RPOD_ECOLI
ID RPOD_ECOLI Reviewed; 613 AA.
AC P00579; Q2M9D8;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 209.
DE RecName: Full=RNA polymerase sigma factor RpoD {ECO:0000255|HAMAP-Rule:MF_00963};
DE AltName: Full=Sigma-70 {ECO:0000255|HAMAP-Rule:MF_00963};
GN Name=rpoD {ECO:0000255|HAMAP-Rule:MF_00963}; Synonyms=alt;
GN OrderedLocusNames=b3067, JW3039;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=6269063; DOI=10.1093/nar/9.12.2889;
RA Burton Z.F., Burgess R.R., Lin J., Moore D., Holder S., Gross C.A.;
RT "The nucleotide sequence of the cloned rpoD gene for the RNA polymerase
RT sigma subunit from E coli K12.";
RL Nucleic Acids Res. 9:2889-2903(1981).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 1-4.
RC STRAIN=K12;
RX PubMed=1095419; DOI=10.1016/0014-5793(75)81001-5;
RA Fujiki H., Zurek G.;
RT "The subunits of DNA-dependent RNA polymerase from E. coli: I. Amino acid
RT analysis and primary structure of the N-terminal regions.";
RL FEBS Lett. 55:242-244(1975).
RN [5]
RP FUNCTION.
RC STRAIN=K12 / W3350 / ATCC 27020;
RX PubMed=3543015; DOI=10.1016/s0021-9258(19)75718-4;
RA Fujita N., Nomura T., Ishihama A.;
RT "Promoter selectivity of Escherichia coli RNA polymerase. Purification and
RT properties of holoenzyme containing the heat-shock sigma subunit.";
RL J. Biol. Chem. 262:1855-1859(1987).
RN [6]
RP FUNCTION.
RX PubMed=1745227; DOI=10.1007/bf00290644;
RA Ozaki M., Wada A., Fujita N., Ishihama A.;
RT "Growth phase-dependent modification of RNA polymerase in Escherichia
RT coli.";
RL Mol. Gen. Genet. 230:17-23(1991).
RN [7]
RP FUNCTION, DNA-BINDING, AND DOMAIN.
RX PubMed=1643661; DOI=10.1016/0092-8674(92)90174-b;
RA Dombroski A.J., Walter W.A., Record M.T. Jr., Siegele D.A., Gross C.A.;
RT "Polypeptides containing highly conserved regions of transcription
RT initiation factor sigma 70 exhibit specificity of binding to promoter
RT DNA.";
RL Cell 70:501-512(1992).
RN [8]
RP FUNCTION.
RX PubMed=8289270; DOI=10.1006/jmbi.1994.1001;
RA Kumar A., Grimes B., Fujita N., Makino K., Malloch R.A., Hayward R.S.,
RA Ishihama A.;
RT "Role of the sigma 70 subunit of Escherichia coli RNA polymerase in
RT transcription activation.";
RL J. Mol. Biol. 235:405-413(1994).
RN [9]
RP FUNCTION.
RC STRAIN=K12;
RX PubMed=8808934; DOI=10.1128/jb.178.18.5447-5451.1996;
RA Jishage M., Iwata A., Ueda S., Ishihama A.;
RT "Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli:
RT intracellular levels of four species of sigma subunit under various growth
RT conditions.";
RL J. Bacteriol. 178:5447-5451(1996).
RN [10]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [11]
RP PROBABLE INTERACTION WITH CRP, AND MUTAGENESIS OF ARG-596.
RX PubMed=10860740; DOI=10.1006/jmbi.2000.3737;
RA Rhodius V.A., Busby S.J.;
RT "Interactions between activating region 3 of the Escherichia coli cyclic
RT AMP receptor protein and region 4 of the RNA polymerase sigma(70) subunit:
RT application of suppression genetics.";
RL J. Mol. Biol. 299:311-324(2000).
RN [12]
RP FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=21398637; DOI=10.1093/nar/gkr129;
RA Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P.;
RT "In vitro transcription profiling of the sigmaS subunit of bacterial RNA
RT polymerase: re-definition of the sigmaS regulon and identification of
RT sigmaS-specific promoter sequence elements.";
RL Nucleic Acids Res. 39:5338-5355(2011).
RN [13]
RP INTERACTION WITH ESCHERICHIA PHAGE LAMBDA ANTITERMINATION PROTEIN Q
RP (MICROBIAL INFECTION), AND MUTAGENESIS OF ALA-553.
RX PubMed=24440517; DOI=10.1016/j.str.2013.12.010;
RA Vorobiev S.M., Gensler Y., Vahedian-Movahed H., Seetharaman J., Su M.,
RA Huang J.Y., Xiao R., Kornhaber G., Montelione G.T., Tong L., Ebright R.H.,
RA Nickels B.E.;
RT "Structure of the DNA-binding and RNA-polymerase-binding region of
RT transcription antitermination factor lambdaQ.";
RL Structure 22:488-495(2014).
RN [14] {ECO:0007744|PDB:1SIG}
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 114-448.
RX PubMed=8858155; DOI=10.1016/s0092-8674(00)81329-x;
RA Malhotra A., Severinova E., Darst S.A.;
RT "Crystal structure of a sigma 70 subunit fragment from E. coli RNA
RT polymerase.";
RL Cell 87:127-136(1996).
RN [15] {ECO:0007744|PDB:1TLH}
RP STRUCTURE BY NMR OF 533-613 IN COMPLEX WITH PHAGE T4 PROTEIN ASIA, AND
RP SUBUNIT.
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 [16]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 546-613 IN COMPLEX WITH RSD, AND
RP SUBUNIT.
RX PubMed=17681541; DOI=10.1016/j.jmb.2007.06.081;
RA Patikoglou G.A., Westblade L.F., Campbell E.A., Lamour V., Lane W.J.,
RA Darst S.A.;
RT "Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in
RT complex with sigma70 domain 4.";
RL J. Mol. Biol. 372:649-659(2007).
RN [17] {ECO:0007744|PDB:3IYD}
RP STRUCTURE BY ELECTRON MICROSCOPY (19.80 ANGSTROMS) IN COMPLEX WITH RPOA;
RP RPOB; RPOC; RPOZ; CRP AND DNA, DOMAIN, DNA-BINDING, AND SUBUNIT.
RX PubMed=19903881; DOI=10.1073/pnas.0908782106;
RA Hudson B.P., Quispe J., Lara-Gonzalez S., Kim Y., Berman H.M., Arnold E.,
RA Ebright R.H., Lawson C.L.;
RT "Three-dimensional EM structure of an intact activator-dependent
RT transcription initiation complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:19830-19835(2009).
RN [18] {ECO:0007744|PDB:3T72}
RP X-RAY CRYSTALLOGRAPHY (4.33 ANGSTROMS) OF 533-609 IN COMPLEX WITH RPOB;
RP PHOB AND PHO BOX DNA, DNA-BINDING, SUBUNIT, AND DOMAIN.
RX PubMed=21829166; DOI=10.1038/emboj.2011.271;
RA Blanco A.G., Canals A., Bernues J., Sola M., Coll M.;
RT "The structure of a transcription activation subcomplex reveals how
RT sigma(70) is recruited to PhoB promoters.";
RL EMBO J. 30:3776-3785(2011).
RN [19] {ECO:0007744|PDB:4YG2}
RP X-RAY CRYSTALLOGRAPHY (3.70 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC AND
RP RPOZ, AND SUBUNIT.
RX PubMed=23389035; DOI=10.1074/jbc.m112.430900;
RA Murakami K.S.;
RT "X-ray crystal structure of Escherichia coli RNA polymerase sigma70
RT holoenzyme.";
RL J. Biol. Chem. 288:9126-9134(2013).
RN [20] {ECO:0007744|PDB:4MEX, ECO:0007744|PDB:4MEY}
RP X-RAY CRYSTALLOGRAPHY (3.90 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC;
RP RPOZ AND SALINAMIDE A, FUNCTION, AND SUBUNIT.
RX PubMed=24843001; DOI=10.7554/elife.02451;
RA Degen D., Feng Y., Zhang Y., Ebright K.Y., Ebright Y.W., Gigliotti M.,
RA Vahedian-Movahed H., Mandal S., Talaue M., Connell N., Arnold E.,
RA Fenical W., Ebright R.H.;
RT "Transcription inhibition by the depsipeptide antibiotic salinamide A.";
RL Elife 3:e02451-e02451(2014).
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. Preferentially transcribes genes associated with
CC fast growth, such as ribosomal operons, other protein-synthesis related
CC genes, rRNA- and tRNA-encoding genes and prfB. {ECO:0000255|HAMAP-
CC Rule:MF_00963, ECO:0000269|PubMed:1643661, ECO:0000269|PubMed:1745227,
CC ECO:0000269|PubMed:21398637, ECO:0000269|PubMed:24843001,
CC ECO:0000269|PubMed:3543015, ECO:0000269|PubMed:8289270,
CC ECO:0000269|PubMed:8808934}.
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. Identified in a complex containing RpoD, the RNA
CC polymerase subunits RpoA, RpoB and RpoZ, CRP and DNA. Interacts with
CC Rsd; this prevents interaction with the RNA polymerase catalytic core
CC and with promoter DNA, and as a consequence, promotes transcription
CC from promoters that require alternative sigma factors. Interacts with
CC phage T4 AsiA; this interferes with binding to DNA and to the RNA
CC polymerase. {ECO:0000255|HAMAP-Rule:MF_00963,
CC ECO:0000269|PubMed:15257291, ECO:0000269|PubMed:17681541,
CC ECO:0000269|PubMed:19903881, ECO:0000269|PubMed:21829166,
CC ECO:0000269|PubMed:23389035, ECO:0000269|PubMed:24843001}.
CC -!- SUBUNIT: (Microbial infection) Interacts with Escherichia phage lambda
CC antitermination protein Q. {ECO:0000269|PubMed:24440517}.
CC -!- INTERACTION:
CC P00579; P0A8V2: rpoB; NbExp=10; IntAct=EBI-545104, EBI-544996;
CC P00579; P0A8T7: rpoC; NbExp=11; IntAct=EBI-545104, EBI-543604;
CC P00579; P0AFX4: rsd; NbExp=11; IntAct=EBI-545104, EBI-1134364;
CC P00579; P32267: asiA; Xeno; NbExp=7; IntAct=EBI-545104, EBI-2124737;
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 -!- 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:0000305}.
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 -!- 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:19903881 and PubMed:21829166). This
CC domain is probably also responsible for interaction with Crp
CC (PubMed:10860740). {ECO:0000269|PubMed:10860740}.
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; J01687; AAA24601.1; -; Genomic_DNA.
DR EMBL; U28379; AAA89147.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76103.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77118.1; -; Genomic_DNA.
DR PIR; A65095; RNECS.
DR RefSeq; NP_417539.1; NC_000913.3.
DR RefSeq; WP_000437376.1; NZ_LN832404.1.
DR PDB; 1SIG; X-ray; 2.60 A; A=114-448.
DR PDB; 1TLH; NMR; -; B=533-613.
DR PDB; 2P7V; X-ray; 2.60 A; B=546-613.
DR PDB; 3IYD; EM; 19.80 A; F=1-613.
DR PDB; 3T72; X-ray; 4.33 A; o/q=533-609.
DR PDB; 4JK1; X-ray; 3.90 A; X/Y=1-613.
DR PDB; 4JK2; X-ray; 4.20 A; X/Y=1-613.
DR PDB; 4JKR; X-ray; 4.20 A; F/L=1-613.
DR PDB; 4KMU; X-ray; 3.85 A; X/Y=1-613.
DR PDB; 4KN4; X-ray; 3.96 A; X/Y=1-613.
DR PDB; 4KN7; X-ray; 3.69 A; X/Y=1-613.
DR PDB; 4LJZ; X-ray; 3.59 A; F/L=92-613.
DR PDB; 4LK0; X-ray; 3.91 A; F/L=92-613.
DR PDB; 4LK1; X-ray; 3.84 A; F/L=1-613.
DR PDB; 4LLG; X-ray; 3.79 A; F/L=1-613.
DR PDB; 4MEX; X-ray; 3.90 A; F/L=1-613.
DR PDB; 4MEY; X-ray; 3.95 A; F/L=1-613.
DR PDB; 4XSX; X-ray; 3.71 A; F/L=92-613.
DR PDB; 4XSY; X-ray; 4.01 A; F/L=92-613.
DR PDB; 4XSZ; X-ray; 3.68 A; F/L=92-613.
DR PDB; 4YFK; X-ray; 3.57 A; F/L=1-613.
DR PDB; 4YFN; X-ray; 3.82 A; F/L=1-613.
DR PDB; 4YFX; X-ray; 3.84 A; F/L=1-613.
DR PDB; 4YG2; X-ray; 3.70 A; F/L=1-613.
DR PDB; 4YLN; X-ray; 5.50 A; F/L/R=1-613.
DR PDB; 4YLO; X-ray; 6.00 A; F/L/R=1-613.
DR PDB; 4YLP; X-ray; 5.50 A; F/L/R=1-613.
DR PDB; 4ZH2; X-ray; 4.20 A; F/L=1-613.
DR PDB; 4ZH3; X-ray; 4.08 A; F/L=1-613.
DR PDB; 4ZH4; X-ray; 3.99 A; F/L=1-613.
DR PDB; 5UAC; X-ray; 3.80 A; F/L=1-613.
DR PDB; 5UAG; X-ray; 3.40 A; F/L=1-613.
DR PDB; 5UAH; X-ray; 4.10 A; F/L=1-613.
DR PDB; 5UAJ; X-ray; 3.92 A; F/L=1-613.
DR PDB; 5UAL; X-ray; 3.89 A; F/L=1-613.
DR PDB; 5UAQ; X-ray; 3.60 A; F/L=1-613.
DR PDB; 5VSW; X-ray; 4.29 A; F/L=1-613.
DR PDB; 5VT0; EM; 3.78 A; L=94-613.
DR PDB; 5W1S; X-ray; 3.81 A; F/L=1-613.
DR PDB; 5W1T; X-ray; 4.50 A; F/L=1-613.
DR PDB; 6B6H; EM; 3.90 A; F=1-613.
DR PDB; 6BYU; X-ray; 3.60 A; F/L=1-613.
DR PDB; 6C9Y; EM; 4.25 A; F=1-613.
DR PDB; 6CA0; EM; 5.75 A; F=1-613.
DR PDB; 6CUX; X-ray; 4.10 A; F/L=1-613.
DR PDB; 6JNX; EM; 4.08 A; F=1-613.
DR PDB; 6K4Y; EM; 3.79 A; F=1-613.
DR PDB; 6LDI; EM; 3.69 A; F=1-613.
DR PDB; 6N4C; EM; 17.00 A; F=8-613.
DR PDB; 6N57; EM; 3.70 A; L=1-613.
DR PDB; 6N58; EM; 3.78 A; L=1-613.
DR PDB; 6OUL; EM; 3.40 A; L=1-613.
DR PDB; 6P18; EM; 3.50 A; F=1-613.
DR PDB; 6P1K; EM; 4.05 A; L=1-613.
DR PDB; 6PB4; EM; 4.35 A; F=1-613.
DR PDB; 6PB5; EM; 4.52 A; F=1-613.
DR PDB; 6PB6; EM; 4.29 A; F=1-613.
DR PDB; 6PSQ; EM; 3.40 A; L=1-613.
DR PDB; 6PSR; EM; 3.40 A; L=1-613.
DR PDB; 6PSS; EM; 3.50 A; L=1-613.
DR PDB; 6PST; EM; 3.00 A; L=1-613.
DR PDB; 6PSU; EM; 3.90 A; L=1-613.
DR PDB; 6PSV; EM; 3.50 A; L=1-613.
DR PDB; 6PSW; EM; 3.70 A; L=1-613.
DR PDB; 6VJS; X-ray; 4.02 A; X/Y=1-613.
DR PDB; 6WMU; EM; 3.18 A; F=1-613.
DR PDB; 6XH7; EM; 3.90 A; F=1-613.
DR PDB; 6XH8; EM; 4.10 A; F=1-613.
DR PDB; 6XL5; EM; 2.50 A; F=1-613.
DR PDB; 6XL9; EM; 2.50 A; F=1-613.
DR PDB; 6XLJ; EM; 2.70 A; F=1-613.
DR PDB; 6XLL; EM; 2.70 A; F=1-613.
DR PDB; 6XLM; EM; 3.20 A; F=1-613.
DR PDB; 7BEF; EM; 4.50 A; F=1-613.
DR PDB; 7C17; EM; 4.22 A; F=1-613.
DR PDB; 7C97; EM; 3.68 A; F=1-613.
DR PDB; 7CHW; EM; 3.58 A; F=1-613.
DR PDB; 7DY6; EM; 3.68 A; F=1-613.
DR PDB; 7KHB; EM; 3.53 A; F=1-613.
DR PDB; 7KHC; EM; 4.14 A; F=1-613.
DR PDB; 7KHE; EM; 3.58 A; F=1-613.
DR PDB; 7KHI; EM; 3.62 A; F=1-613.
DR PDBsum; 1SIG; -.
DR PDBsum; 1TLH; -.
DR PDBsum; 2P7V; -.
DR PDBsum; 3IYD; -.
DR PDBsum; 3T72; -.
DR PDBsum; 4JK1; -.
DR PDBsum; 4JK2; -.
DR PDBsum; 4JKR; -.
DR PDBsum; 4KMU; -.
DR PDBsum; 4KN4; -.
DR PDBsum; 4KN7; -.
DR PDBsum; 4LJZ; -.
DR PDBsum; 4LK0; -.
DR PDBsum; 4LK1; -.
DR PDBsum; 4LLG; -.
DR PDBsum; 4MEX; -.
DR PDBsum; 4MEY; -.
DR PDBsum; 4XSX; -.
DR PDBsum; 4XSY; -.
DR PDBsum; 4XSZ; -.
DR PDBsum; 4YFK; -.
DR PDBsum; 4YFN; -.
DR PDBsum; 4YFX; -.
DR PDBsum; 4YG2; -.
DR PDBsum; 4YLN; -.
DR PDBsum; 4YLO; -.
DR PDBsum; 4YLP; -.
DR PDBsum; 4ZH2; -.
DR PDBsum; 4ZH3; -.
DR PDBsum; 4ZH4; -.
DR PDBsum; 5UAC; -.
DR PDBsum; 5UAG; -.
DR PDBsum; 5UAH; -.
DR PDBsum; 5UAJ; -.
DR PDBsum; 5UAL; -.
DR PDBsum; 5UAQ; -.
DR PDBsum; 5VSW; -.
DR PDBsum; 5VT0; -.
DR PDBsum; 5W1S; -.
DR PDBsum; 5W1T; -.
DR PDBsum; 6B6H; -.
DR PDBsum; 6BYU; -.
DR PDBsum; 6C9Y; -.
DR PDBsum; 6CA0; -.
DR PDBsum; 6CUX; -.
DR PDBsum; 6JNX; -.
DR PDBsum; 6K4Y; -.
DR PDBsum; 6LDI; -.
DR PDBsum; 6N4C; -.
DR PDBsum; 6N57; -.
DR PDBsum; 6N58; -.
DR PDBsum; 6OUL; -.
DR PDBsum; 6P18; -.
DR PDBsum; 6P1K; -.
DR PDBsum; 6PB4; -.
DR PDBsum; 6PB5; -.
DR PDBsum; 6PB6; -.
DR PDBsum; 6PSQ; -.
DR PDBsum; 6PSR; -.
DR PDBsum; 6PSS; -.
DR PDBsum; 6PST; -.
DR PDBsum; 6PSU; -.
DR PDBsum; 6PSV; -.
DR PDBsum; 6PSW; -.
DR PDBsum; 6VJS; -.
DR PDBsum; 6WMU; -.
DR PDBsum; 6XH7; -.
DR PDBsum; 6XH8; -.
DR PDBsum; 6XL5; -.
DR PDBsum; 6XL9; -.
DR PDBsum; 6XLJ; -.
DR PDBsum; 6XLL; -.
DR PDBsum; 6XLM; -.
DR PDBsum; 7BEF; -.
DR PDBsum; 7C17; -.
DR PDBsum; 7C97; -.
DR PDBsum; 7CHW; -.
DR PDBsum; 7DY6; -.
DR PDBsum; 7KHB; -.
DR PDBsum; 7KHC; -.
DR PDBsum; 7KHE; -.
DR PDBsum; 7KHI; -.
DR AlphaFoldDB; P00579; -.
DR BMRB; P00579; -.
DR SMR; P00579; -.
DR BioGRID; 4261068; 200.
DR BioGRID; 851883; 14.
DR ComplexPortal; CPX-4881; DNA-directed RNA polymerase holoenzyme complex, Sigma70 variant.
DR ComplexPortal; CPX-4901; rpod-rsd sigma-antisigma complex.
DR DIP; DIP-10773N; -.
DR IntAct; P00579; 56.
DR STRING; 511145.b3067; -.
DR jPOST; P00579; -.
DR PaxDb; P00579; -.
DR PRIDE; P00579; -.
DR EnsemblBacteria; AAC76103; AAC76103; b3067.
DR EnsemblBacteria; BAE77118; BAE77118; BAE77118.
DR GeneID; 947567; -.
DR KEGG; ecj:JW3039; -.
DR KEGG; eco:b3067; -.
DR PATRIC; fig|1411691.4.peg.3662; -.
DR EchoBASE; EB0889; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_7_2_6; -.
DR InParanoid; P00579; -.
DR OMA; RDAKKEM; -.
DR PhylomeDB; P00579; -.
DR BioCyc; EcoCyc:RPOD-MON; -.
DR BioCyc; MetaCyc:RPOD-MON; -.
DR EvolutionaryTrace; P00579; -.
DR PRO; PR:P00579; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0000345; C:cytosolic DNA-directed RNA polymerase complex; IPI:ComplexPortal.
DR GO; GO:1903865; C:sigma factor antagonist complex; IPI:ComplexPortal.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016987; F:sigma factor activity; IDA:EcoliWiki.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:UniProtKB-UniRule.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IC:ComplexPortal.
DR GO; GO:2000142; P:regulation of DNA-templated transcription, initiation; IDA:ComplexPortal.
DR GO; GO:0009408; P:response to heat; IEP:EcoliWiki.
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; IPR007631; RNA_pol_sigma_70_non-ess.
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; PF04546; Sigma70_ner; 1.
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; Direct protein sequencing; DNA-binding;
KW Reference proteome; Sigma factor; Transcription; Transcription regulation.
FT CHAIN 1..613
FT /note="RNA polymerase sigma factor RpoD"
FT /id="PRO_0000093885"
FT DNA_BIND 573..592
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 2..80
FT /note="Sigma-70 factor domain-1"
FT REGION 176..213
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 379..449
FT /note="Sigma-70 factor domain-2"
FT REGION 458..534
FT /note="Sigma-70 factor domain-3"
FT REGION 547..600
FT /note="Sigma-70 factor domain-4"
FT REGION 584..599
FT /note="Interaction with anti-sigma factors"
FT MOTIF 403..406
FT /note="Interaction with polymerase core subunit RpoC"
FT COMPBIAS 187..210
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT SITE 562
FT /note="Interaction with anti-sigma factors"
FT MUTAGEN 553
FT /note="A->D: Disrupts the interaction with Escherichia
FT phage lambda antitermination protein Q."
FT /evidence="ECO:0000269|PubMed:24440517"
FT MUTAGEN 596
FT /note="R->D,E: 2-fold reduction in activation of class II
FT Crp-dependent promoters."
FT /evidence="ECO:0000269|PubMed:10860740"
FT CONFLICT 149
FT /note="D -> N (in Ref. 1; AAA24601)"
FT /evidence="ECO:0000305"
FT HELIX 8..19
FT /evidence="ECO:0007829|PDB:6PST"
FT HELIX 24..30
FT /evidence="ECO:0007829|PDB:6PST"
FT HELIX 39..50
FT /evidence="ECO:0007829|PDB:6PST"
FT STRAND 55..58
FT /evidence="ECO:0007829|PDB:6PST"
FT HELIX 62..67
FT /evidence="ECO:0007829|PDB:6PST"
FT TURN 71..74
FT /evidence="ECO:0007829|PDB:6PSS"
FT HELIX 75..87
FT /evidence="ECO:0007829|PDB:6PST"
FT HELIX 97..105
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 106..108
FT /evidence="ECO:0007829|PDB:6XL9"
FT HELIX 113..134
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 138..152
FT /evidence="ECO:0007829|PDB:6XL5"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:6PST"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 162..165
FT /evidence="ECO:0007829|PDB:6XL5"
FT TURN 179..182
FT /evidence="ECO:0007829|PDB:1SIG"
FT TURN 187..190
FT /evidence="ECO:0007829|PDB:1SIG"
FT HELIX 214..232
FT /evidence="ECO:0007829|PDB:6XL5"
FT TURN 237..240
FT /evidence="ECO:0007829|PDB:6XL9"
FT HELIX 245..256
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 259..261
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 263..294
FT /evidence="ECO:0007829|PDB:6XL5"
FT TURN 302..305
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 306..309
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 310..312
FT /evidence="ECO:0007829|PDB:6WMU"
FT TURN 313..316
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 317..320
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:6PST"
FT HELIX 325..329
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 330..333
FT /evidence="ECO:0007829|PDB:6XL5"
FT TURN 334..337
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 338..341
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 344..351
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 355..382
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 384..391
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 392..394
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 397..399
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 401..418
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 421..423
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 427..446
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 447..450
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 454..474
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 480..486
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 487..489
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 491..500
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 506..508
FT /evidence="ECO:0007829|PDB:6PSS"
FT HELIX 511..513
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 515..518
FT /evidence="ECO:0007829|PDB:6XLJ"
FT HELIX 519..522
FT /evidence="ECO:0007829|PDB:6XL5"
FT STRAND 526..528
FT /evidence="ECO:0007829|PDB:5UAG"
FT HELIX 531..549
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 553..562
FT /evidence="ECO:0007829|PDB:6XL5"
FT TURN 563..566
FT /evidence="ECO:0007829|PDB:6PST"
FT STRAND 567..569
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 573..580
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 584..599
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 601..604
FT /evidence="ECO:0007829|PDB:6XL5"
FT TURN 605..607
FT /evidence="ECO:0007829|PDB:6XL5"
FT HELIX 608..610
FT /evidence="ECO:0007829|PDB:6XL5"
SQ SEQUENCE 613 AA; 70263 MW; CA4F0E30DEC1703D CRC64;
MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP
DADDLMLAEN TADEDAAEAA AQVLSSVESE IGRTTDPVRM YMREMGTVEL LTREGEIDIA
KRIEDGINQV QCSVAEYPEA ITYLLEQYDR VEAEEARLSD LITGFVDPNA EEDLAPTATH
VGSELSQEDL DDDEDEDEED GDDDSADDDN SIDPELAREK FAELRAQYVV TRDTIKAKGR
SHATAQEEIL KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK
NFITLFTGNE TSDTWFNAAI AMNKPWSEKL HDVSEEVHRA LQKLQQIEEE TGLTIEQVKD
INRRMSIGEA KARRAKKEMV EANLRLVISI AKKYTNRGLQ FLDLIQEGNI GLMKAVDKFE
YRRGYKFSTY ATWWIRQAIT RSIADQARTI RIPVHMIETI NKLNRISRQM LQEMGREPTP
EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL
RAATHDVLAG LTAREAKVLR MRFGIDMNTD YTLEEVGKQF DVTRERIRQI EAKALRKLRH
PSRSEVLRSF LDD
