RPOD_RHIME
ID RPOD_RHIME Reviewed; 684 AA.
AC Q59753;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=RNA polymerase sigma factor RpoD {ECO:0000255|HAMAP-Rule:MF_00963};
DE Short=Sigma-A;
DE AltName: Full=Major vegetative sigma factor;
GN Name=rpoD {ECO:0000255|HAMAP-Rule:MF_00963}; Synonyms=sigA;
GN OrderedLocusNames=R02314; ORFNames=SMc01563;
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=7592490; DOI=10.1128/jb.177.23.6952-6957.1995;
RA Rushing B.G., Long S.R.;
RT "Cloning and characterization of the sigA gene encoding the major sigma
RT subunit of Rhizobium meliloti.";
RL J. Bacteriol. 177:6952-6957(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11481430; DOI=10.1073/pnas.161294398;
RA Capela D., Barloy-Hubler F., Gouzy J., Bothe G., Ampe F., Batut J.,
RA Boistard P., Becker A., Boutry M., Cadieu E., Dreano S., Gloux S.,
RA Godrie T., Goffeau A., Kahn D., Kiss E., Lelaure V., Masuy D., Pohl T.,
RA Portetelle D., Puehler A., Purnelle B., Ramsperger U., Renard C.,
RA Thebault P., Vandenbol M., Weidner S., Galibert F.;
RT "Analysis of the chromosome sequence of the legume symbiont Sinorhizobium
RT meliloti strain 1021.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9877-9882(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11474104; DOI=10.1126/science.1060966;
RA Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA Wong K., Yeh K.-C., Batut J.;
RT "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL Science 293:668-672(2001).
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 -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00963}.
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DR EMBL; L47288; AAA88524.1; -; Genomic_DNA.
DR EMBL; AL591688; CAC46893.1; -; Genomic_DNA.
DR RefSeq; NP_386420.1; NC_003047.1.
DR RefSeq; WP_003532953.1; NC_003047.1.
DR AlphaFoldDB; Q59753; -.
DR SMR; Q59753; -.
DR STRING; 266834.SMc01563; -.
DR EnsemblBacteria; CAC46893; CAC46893; SMc01563.
DR GeneID; 61603780; -.
DR KEGG; sme:SMc01563; -.
DR PATRIC; fig|266834.11.peg.3792; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_7_2_5; -.
DR OMA; IYAYKDA; -.
DR Proteomes; UP000001976; 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; 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 3: Inferred from homology;
KW Cytoplasm; DNA-binding; Reference proteome; Sigma factor; Transcription;
KW Transcription regulation.
FT CHAIN 1..684
FT /note="RNA polymerase sigma factor RpoD"
FT /id="PRO_0000093908"
FT DNA_BIND 644..663
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 83..128
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 203..262
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 450..520
FT /note="Sigma-70 factor domain-2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 529..605
FT /note="Sigma-70 factor domain-3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 618..671
FT /note="Sigma-70 factor domain-4"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT MOTIF 474..477
FT /note="Interaction with polymerase core subunit RpoC"
FT COMPBIAS 83..100
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 214..237
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 684 AA; 77174 MW; 297E53CCD9FF4EF5 CRC64;
MATKVKENEE ADVEREGAPD GPLLDLSDDA VKKMIKAAKK RGYVTMDELN SVLPSEEVTS
EQIEDTMSML SDMGINVIED EEAEEAAASD DDDGADEGES EGGELAPASG TALAASKKKE
PTDRTDDPVR MYLREMGSVE LLSREGEIAI AKRIEAGRET MIAGLCESPL TFQALIIWRD
ELNEGQTLLR EIIDLETTYS GPEAKAAPQF QSPEKIEADR KAAEEKEKVR RTRTAANDDD
ITNVGGEGQA PEEEEEDDDE SNLSLAAMEA ELRPQVMETL DVIAETYKKL RKLQDQQVEA
RLAATGTLSP AQERRYKELK DELIKAVKSL SLNQNRIDAL VEQLYDISKR LTQNEGRLLR
LAESYGVKRE AFLEQYSGAE LDPNWMKSIS NLAGKGWKEF ARAENQTIRD IRQEIQNLAT
ETGISIAEFR RIVSMVQKGE REARIAKKEM VEANLRLVIS IAKKYTNRGL QFLDLIQEGN
IGLMKAVDKF EYRRGYKFST YATWWIRQAI TRSIADQART IRIPVHMIET INKIVRTSRQ
MLHEIGREPT PEELAEKLAM PLEKVRKVLK IAKEPISLET PVGDEEDSHL GDFIEDKNAL
LPIDAAIQAN LRETTTRVLA SLTPREERVL RMRFGIGMNT DHTLEEVGQQ FSVTRERIRQ
IEAKALRKLK HPSRSRKLRS FLDS
