ID S5YCU8_PARAH Unreviewed; 662 AA.
AC S5YCU8;
DT 16-OCT-2013, integrated into UniProtKB/TrEMBL.
DT 16-OCT-2013, sequence version 1.
DT 24-JAN-2024, entry version 57.
DE RecName: Full=RNA polymerase sigma factor RpoD {ECO:0000256|HAMAP-Rule:MF_00963};
DE AltName: Full=Sigma-70 {ECO:0000256|HAMAP-Rule:MF_00963};
GN Name=rpoD {ECO:0000256|HAMAP-Rule:MF_00963};
GN ORFNames=JCM7686_2204 {ECO:0000313|EMBL:AGT09283.1};
OS Paracoccus aminophilus JCM 7686.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Paracoccaceae; Paracoccus.
OX NCBI_TaxID=1367847 {ECO:0000313|EMBL:AGT09283.1, ECO:0000313|Proteomes:UP000015480};
RN [1] {ECO:0000313|EMBL:AGT09283.1, ECO:0000313|Proteomes:UP000015480}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 7686 {ECO:0000313|EMBL:AGT09283.1};
RX PubMed=24517536; DOI=10.1186/1471-2164-15-124;
RA Dziewit L., Czarnecki J., Wibberg D., Radlinska M., Mrozek P., Szymczak M.,
RA Schluter A., Puhler A., Bartosik D.;
RT "Architecture and functions of a multipartite genome of the methylotrophic
RT bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary
RT chromids.";
RL BMC Genomics 15:124-124(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. {ECO:0000256|HAMAP-Rule:MF_00963}.
CC -!- SUBUNIT: Interacts transiently with the RNA polymerase catalytic core.
CC {ECO:0000256|HAMAP-Rule:MF_00963}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00963}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA subfamily.
CC {ECO:0000256|HAMAP-Rule:MF_00963}.
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DR EMBL; CP006650; AGT09283.1; -; Genomic_DNA.
DR RefSeq; WP_020950921.1; NC_022041.1.
DR AlphaFoldDB; S5YCU8; -.
DR STRING; 1367847.JCM7686_2204; -.
DR KEGG; pami:JCM7686_2204; -.
DR PATRIC; fig|1367847.3.peg.2197; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_7_2_5; -.
DR OrthoDB; 9809557at2; -.
DR Proteomes; UP000015480; 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 CDD; cd06171; Sigma70_r4; 1.
DR Gene3D; 1.10.601.10; RNA Polymerase Primary Sigma Factor; 1.
DR Gene3D; 1.10.220.120; Sigma-70 factor, region 1.1; 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; 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 NCBIfam; TIGR02393; RpoD_Cterm; 1.
DR NCBIfam; TIGR02937; sigma70-ECF; 1.
DR PANTHER; PTHR30603; RNA POLYMERASE SIGMA FACTOR RPO; 1.
DR PANTHER; PTHR30603:SF60; RNA POLYMERASE SIGMA FACTOR RPOD; 1.
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; SSF88946; Sigma2 domain of RNA polymerase sigma factors; 1.
DR SUPFAM; SSF88659; Sigma3 and sigma4 domains of RNA polymerase sigma factors; 2.
DR PROSITE; PS00715; SIGMA70_1; 1.
DR PROSITE; PS00716; SIGMA70_2; 1.
PE 3: Inferred from homology;
KW Coiled coil {ECO:0000256|SAM:Coils};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00963};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_00963}; Reference proteome {ECO:0000313|Proteomes:UP000015480};
KW Sigma factor {ECO:0000256|ARBA:ARBA00023082, ECO:0000256|HAMAP-
KW Rule:MF_00963};
KW Transcription {ECO:0000256|ARBA:ARBA00023163, ECO:0000256|HAMAP-
KW Rule:MF_00963};
KW Transcription regulation {ECO:0000256|ARBA:ARBA00023015, ECO:0000256|HAMAP-
KW Rule:MF_00963}.
FT DOMAIN 452..465
FT /note="RNA polymerase sigma-70"
FT /evidence="ECO:0000259|PROSITE:PS00715"
FT DOMAIN 621..647
FT /note="RNA polymerase sigma-70"
FT /evidence="ECO:0000259|PROSITE:PS00716"
FT DNA_BIND 622..641
FT /note="H-T-H motif"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 74..110
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 194..239
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 428..498
FT /note="Sigma-70 factor domain-2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT REGION 507..583
FT /note="Sigma-70 factor domain-3"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT REGION 596..649
FT /note="Sigma-70 factor domain-4"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT COILED 407..434
FT /evidence="ECO:0000256|SAM:Coils"
FT MOTIF 452..455
FT /note="Interaction with polymerase core subunit RpoC"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00963"
FT COMPBIAS 1..23
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 85..101
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 662 AA; 75304 MW; E0790F2D70D4D588 CRC64;
MASKDDDDNK PDTKDDEHSL DMSQTAVKRM IAEGRERGFI TYDQLNAVLP PDQVSSDQIE
DVMSMLSEMD IRVVESDEDS DDSETGGQLA TTGSGSREVA LATTETEKLD RTDDPVRMYL
REMGSVELLS REGEIAIAKR IEAGRNTMIA GLCESPLTFK AITMWREELL DEDILLRDVI
DLEATFGRVL DEEGEDTELE TAEPVVGAAP AQARTGDEEF DADGNPMRRE DEEDDEDGQS
LSLAAMEASL KPKVLETLEQ IAHGYEELAH MQDSRMSATL NEDSTFSASD ELAYQRKRSE
IVLLVNELHL HNNRIEALVD QIYGINRRIL TIDSGMVKLA DAARINRQEF IKAYRGCELD
PTWVDRMSSG TSRGWQTLFD KSRDQVDRLR GDMADVGQYV GVDIEEFRRI VNQVQRGEKE
ARQAKKEMVE ANLRLVISIA KKYTNRGLQF LDLIQEGNIG LMKAVDKFEY RRGYKFSTYA
TWWIRQAITR SIADQARTIR IPVHMIETIN KLVRTGRQML HEIGREPTPE ELAEKLQMPL
EKVRKVMKIA KEPISLETPI GDEEDSQLGD FIEDKNAVLP LESAIQENLK ETTTRVLASL
TPREERVLRM RFGIGMNTDH TLEEVGQQFS VTRERIRQIE AKALRKLKHP SRSRKLRSFL
DQ
//