RPOD_XYLFA
ID RPOD_XYLFA Reviewed; 618 AA.
AC Q9PDM9; Q93LI8;
DT 23-JAN-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 132.
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=XF_1350;
OS Xylella fastidiosa (strain 9a5c).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xylella.
OX NCBI_TaxID=160492;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=9a5c;
RX PubMed=10910347; DOI=10.1038/35018003;
RA Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M.,
RA Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S.,
RA Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S.,
RA Bueno M.R.P., Camargo A.A., Camargo L.E.A., Carraro D.M., Carrer H.,
RA Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M.,
RA Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H.,
RA Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S.,
RA Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H.,
RA Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D.,
RA Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E.,
RA Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F.,
RA Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N.,
RA Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F.,
RA Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y.,
RA Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O.,
RA Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A.,
RA de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R.,
RA Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B.,
RA Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G.,
RA Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M.,
RA da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z.,
RA Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D.,
RA Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S.,
RA Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.;
RT "The genome sequence of the plant pathogen Xylella fastidiosa.";
RL Nature 406:151-159(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 475-618.
RC STRAIN=Citrus;
RA Wendland A., Camargo L.E.;
RT "Sequence of the genomic fragment of Xylella fastidosa amplified with the
RT primers RST31/33.";
RL Submitted (JUN-2001) to the EMBL/GenBank/DDBJ databases.
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; AE003849; AAF84159.1; -; Genomic_DNA.
DR EMBL; AY039798; AAK73284.1; -; Genomic_DNA.
DR PIR; E82691; E82691.
DR RefSeq; WP_010893854.1; NC_002488.3.
DR AlphaFoldDB; Q9PDM9; -.
DR SMR; Q9PDM9; -.
DR STRING; 160492.XF_1350; -.
DR EnsemblBacteria; AAF84159; AAF84159; XF_1350.
DR KEGG; xfa:XF_1350; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_7_0_6; -.
DR OMA; RDAKKEM; -.
DR Proteomes; UP000000812; 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..618
FT /note="RNA polymerase sigma factor RpoD"
FT /id="PRO_0000093933"
FT DNA_BIND 577..596
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 197..217
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 383..453
FT /note="Sigma-70 factor domain-2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 462..538
FT /note="Sigma-70 factor domain-3"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 551..604
FT /note="Sigma-70 factor domain-4"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT MOTIF 407..410
FT /note="Interaction with polymerase core subunit RpoC"
SQ SEQUENCE 618 AA; 69907 MW; F9B8DB0C2A41ABFA CRC64;
MSNERTAQQS DIKQLISKGL EQGYLTYAEV NDHLPEDLVD PDQIEDIIGM INGMGIEVHE
VAPDAETLLL NEGNTGNREV DDTAAEEAAA ALSALDTEAG RTTDPVRMYM REMGTVELLT
REGEIAIAKR IEEGLSEVQA ALGVFPLSTE LLLSEYELHK EGKRRLTEVV VGFNDLIEED
NSVTSSVDVT DESIVEVDEE DDDSVGNDED APTIGPDPAE VASRIESLST EYAKFKKLYA
KHGPEHKAVI KVREDVAAIF VTFKLSLPLT DLLVQQLQNM VNSVKDHERK VLHLATNVAK
MPRKDFIRSW ENNQTNLEWV EDAIKRKQKW SSALRDIKDQ ITAEQQASID LEKANSLTLA
DIKEINRMMV YGEAKASKAK KEMVEANLRL VISIAKKYTN RGLQFLDLIQ EGNIGLMKAV
CKFEHRRGFK FSTYATWWIR QAITRSIADQ ARTIRIPVHM IETINKLNRI SRQMLQQFGR
EATPEELAKE MDMPEDKIRK VMKIAKEPIS METPIGDDED SHLGDFIEDP NVESPVDTTT
NVNLSETVRE VLAGLTPREA KVLRMRFGID MNTDHTLEEV GKQFDVTRER IRQIEAKALR
KLRHPSRSEQ LRSFLDID
