RPOD_AGRFC
ID RPOD_AGRFC Reviewed; 684 AA.
AC P33452;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 27-MAR-2002, sequence version 2.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=RNA polymerase sigma factor RpoD {ECO:0000255|HAMAP-Rule:MF_00963};
DE AltName: Full=Major vegetative sigma factor;
DE AltName: Full=Sigma-70 {ECO:0000255|HAMAP-Rule:MF_00963};
GN Name=rpoD {ECO:0000255|HAMAP-Rule:MF_00963}; Synonyms=sigA;
GN OrderedLocusNames=Atu2167; ORFNames=AGR_C_3929;
OS Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS (strain C58)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=176299;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8491721; DOI=10.1128/jb.175.10.3026-3030.1993;
RA Segal G., Ron E.Z.;
RT "Cloning, sequencing, and transcriptional analysis of the gene coding for
RT the vegetative sigma factor of Agrobacterium tumefaciens.";
RL J. Bacteriol. 175:3026-3030(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743193; DOI=10.1126/science.1066804;
RA Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA Gordon M.P., Olson M.V., Nester E.W.;
RT "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT C58.";
RL Science 294:2317-2323(2001).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743194; DOI=10.1126/science.1066803;
RA Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT "Genome sequence of the plant pathogen and biotechnology agent
RT Agrobacterium tumefaciens C58.";
RL Science 294:2323-2328(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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; X69388; CAA49185.1; -; Genomic_DNA.
DR EMBL; AE007869; AAK87912.1; -; Genomic_DNA.
DR PIR; A36913; RNAGVS.
DR PIR; AF2842; AF2842.
DR PIR; G97619; G97619.
DR RefSeq; NP_355127.1; NC_003062.2.
DR RefSeq; WP_010972109.1; NC_003062.2.
DR AlphaFoldDB; P33452; -.
DR SMR; P33452; -.
DR STRING; 176299.Atu2167; -.
DR EnsemblBacteria; AAK87912; AAK87912; Atu2167.
DR GeneID; 66222367; -.
DR KEGG; atu:Atu2167; -.
DR PATRIC; fig|176299.10.peg.2177; -.
DR eggNOG; COG0568; Bacteria.
DR HOGENOM; CLU_014793_7_1_5; -.
DR OMA; IYAYKDA; -.
DR PhylomeDB; P33452; -.
DR BioCyc; AGRO:ATU2167-MON; -.
DR Proteomes; UP000000813; Chromosome circular.
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_0000093871"
FT DNA_BIND 644..663
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 1..25
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 83..129
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..101
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 214..240
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 245..262
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT CONFLICT 147
FT /note="E -> Q (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 189
FT /note="L -> V (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 234
FT /note="A -> G (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 289..290
FT /note="KL -> NV (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 609..610
FT /note="AN -> GF (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 625
FT /note="R -> S (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 633
FT /note="R -> P (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 668..669
FT /note="KL -> NV (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
FT CONFLICT 680
FT /note="S -> T (in Ref. 1; CAA49185)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 684 AA; 77399 MW; EEC37CDB0E9E9467 CRC64;
MATKVKENEE AENERDGATD GPLLDLSDDA VKKMIKAAKK RGYVTMDELN SVLPSEEVTS
EQIEDTMAML SDMGINVIED EDAEEAAPAE DDGDSDNEES EGGELAPSGG TALATAKKKE
PTDRTDDPVR MYLREMGSVE LLSREGEIAI AKRIEAGRET MISGLCESPL TFQALIIWRD
ELNEGTTLLR EIIDLETTYS GPEAKAAPQF QSPEKIEADR KAAEEKEKTR RLRAPTGDED
VTDVGGDGLP PEEEEEDDDE SNLSLAAMEA ELRPQVMETL DTIADTYKKL RKLQDQQVEA
RLACTGTLSS GQERRYKELK DQLITAVKSL SLNQNRIDSL VEQLYDISKR LMQNEGRLLR
LAESYGVKRD SFLEQYHGAE LDPNWMKSIT NLAARGWKEF AREESNTIRE IRQEIQNLST
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
