RPOD_SHEVD
ID RPOD_SHEVD Reviewed; 614 AA.
AC O24744; D4ZGQ0;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 125.
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}; OrderedLocusNames=SVI_0878;
OS Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=637905;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=11272828; DOI=10.1271/bbb.65.190;
RA Nakasone K., Ikegami A., Kato C., Horikoshi K.;
RT "Isolation of the rpoD gene encoding the principal sigma factor of the
RT deep-sea piezophilic bacterium Shewanella violacea strain DSS12 and its
RT overexpression in Escherichia coli.";
RL Biosci. Biotechnol. Biochem. 65:190-193(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10179 / CIP 106290 / LMG 19151 / DSS12;
RX PubMed=20458400; DOI=10.1039/c000396d;
RA Aono E., Baba T., Ara T., Nishi T., Nakamichi T., Inamoto E., Toyonaga H.,
RA Hasegawa M., Takai Y., Okumura Y., Baba M., Tomita M., Kato C., Oshima T.,
RA Nakasone K., Mori H.;
RT "Complete genome sequence and comparative analysis of Shewanella violacea,
RT a psychrophilic and piezophilic bacterium from deep sea floor sediments.";
RL Mol. Biosyst. 6:1216-1226(2010).
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; AB002098; BAA19475.1; -; Genomic_DNA.
DR EMBL; AP011177; BAJ00849.1; -; Genomic_DNA.
DR PIR; JC7652; JC7652.
DR AlphaFoldDB; O24744; -.
DR SMR; O24744; -.
DR STRING; 637905.SVI_0878; -.
DR PRIDE; O24744; -.
DR EnsemblBacteria; BAJ00849; BAJ00849; SVI_0878.
DR KEGG; svo:SVI_0878; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_7_0_6; -.
DR OMA; RDAKKEM; -.
DR Proteomes; UP000002350; 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..614
FT /note="RNA polymerase sigma factor RpoD"
FT /id="PRO_0000093912"
FT DNA_BIND 574..593
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 178..222
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 380..450
FT /note="Sigma-70 factor domain-2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 459..535
FT /note="Sigma-70 factor domain-3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 548..601
FT /note="Sigma-70 factor domain-4"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT MOTIF 404..407
FT /note="Interaction with polymerase core subunit RpoC"
FT COMPBIAS 197..211
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 614 AA; 70031 MW; 652634FE5131AB39 CRC64;
MEHTPQSQLK LLLAKGKEQG YLTYAEVNDH LPADMVDADQ IEDIVQMIND MGIRVYEQAP
DADEIMMTED STDDDAAEEA AAALATVEAE LGRTTDPVRM YMREMGTVEL LTREGEIVIA
KRIEEGIYTV QASVAEYPPA IASILDQFDR YEAEEVRLSD IISGFIDPNA ADIAPTATHI
GSDLSQSERD KDDSKDDSKD DDEDEEEEGP KGPDPEESKE RFTQLREVHE NTLKIIADKG
RGHPEATVAL FEIGELFKEF RLMPKQFDRL VKNMRATMDK VRVQERLIMK LCVEQAKMPK
KNFVKGYTAD ESSIAWFDTE LASKKPYAEG LKMIEPDVRR CRFKLDIIEK ETGLAIASIK
DINRRMSIGE AKARRAKKEM VEANLRLVIS IAKKYTNRGL QFLDLIQEGN IGLMKAVDKF
EYRRGYKFST YATWWIRQAI TRSIADQART IRIPVHMIET INKLNRISRQ MLQEMGREPT
PEELAERMLM PEDKIRKVLK IAKEPISMET PIGDDEDSHL GDFIEDTTLE LPLDSATGES
LRNATHEVLA GLTAREAKVL RMRFGIDMNT DHTLEEVGKQ FDVTRERIRQ IEAKALRKLR
HPSRSEILKS FLDE
