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P00579 (RPOD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 151. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA polymerase sigma factor RpoD
Alternative name(s):
Sigma-70
Gene names
Name:rpoD
Synonyms:alt
Ordered Locus Names:b3067, JW3039
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length613 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth. Preferentially transcribes genes associated with fast growth, such as ribosomal operons, other protein-synthesis related genes, rRNA- and tRNA-encoding genes and prfB. Ref.5 Ref.6 Ref.7 Ref.8 Ref.9 Ref.12

Subunit structure

Interacts transiently with the RNA polymerase catalytic core formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1 omega subunit) to form the RNA polymerase holoenzyme that can initiate transcription. Identified in a complex containing RpoD, the RNA polymerase subunits RpoA, RpoB and RpoZ, CRP and DNA. Interacts with Rsd; this prevents interaction with the RNA polymerase catalytic core and with promoter DNA, and as a consequence, promotes transcription from promoters that require alternative sigma factors. Interacts with phage T4 AsiA; this interferes with binding to DNA and to the RNA polymerase. Ref.11 Ref.14 Ref.15 Ref.16 Ref.17 Ref.18

Subcellular location

Cytoplasm Potential HAMAP-Rule MF_00963.

Domain

Contains 4 domains, connected by flexible linkers. In the active conformation, the domains are in an extended conformation, each making extensive interactions with the RNA polymerase catalytic core. Ref.7 Ref.16 Ref.17

In the autoinhibited state, sigma-70 factor domain-1 packs closely together with sigma-70 factor domains-2 and -4, contrary to the extended conformation that is seen when the protein is part of the RNA polymerase holoenzyme Probable. Ref.7 Ref.16 Ref.17

The sigma-70 factor domain-2 mediates sequence-specific interaction with the -10 element in promoter DNA, and plays an important role in melting the double-stranded DNA and the formation of the transcription bubble. The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC. Ref.7 Ref.16 Ref.17

The sigma-70 factor domain-4 contains a helix-turn-helix (H-T-H) motif that mediates interaction with the -35 element in promoter DNA. The domain also mediates interaction with the RNA polymerase subunit RpoA. Interactions between sigma-70 factor domain-4 and anti-sigma factors prevents interaction of sigma factors with the RNA polymerase catalytic core (Ref.16 and Ref.17). This domain is probably also responsible for interaction with Crp (Ref.11). Ref.7 Ref.16 Ref.17

Sequence similarities

Belongs to the sigma-70 factor family. RpoD/SigA subfamily.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

asiAP322675EBI-545104,EBI-2124737From a different organism.
rpoCP0A8T78EBI-545104,EBI-543604
rsdP0AFX411EBI-545104,EBI-1134364

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 613613RNA polymerase sigma factor RpoD HAMAP-Rule MF_00963
PRO_0000093885

Regions

DNA binding573 – 59220H-T-H motif Ref.7 Ref.16 Ref.17
Region2 – 8079Sigma-70 factor domain-1 HAMAP-Rule MF_00963
Region379 – 44971Sigma-70 factor domain-2 HAMAP-Rule MF_00963
Region458 – 53477Sigma-70 factor domain-3 HAMAP-Rule MF_00963
Region547 – 60054Sigma-70 factor domain-4 HAMAP-Rule MF_00963
Region584 – 59916Interaction with anti-sigma factors HAMAP-Rule MF_00963
Motif403 – 4064Interaction with polymerase core subunit RpoC HAMAP-Rule MF_00963

Sites

Site5621Interaction with anti-sigma factors

Experimental info

Mutagenesis5961R → D or E: 2-fold reduction in activation of class II Crp-dependent promoters. Ref.11
Sequence conflict1491D → N in AAA24601. Ref.1

Secondary structure

.................................................... 613
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00579 [UniParc].

Last modified October 1, 1996. Version 2.
Checksum: CA4F0E30DEC1703D

FASTA61370,263
        10         20         30         40         50         60 
MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP 

        70         80         90        100        110        120 
DADDLMLAEN TADEDAAEAA AQVLSSVESE IGRTTDPVRM YMREMGTVEL LTREGEIDIA 

       130        140        150        160        170        180 
KRIEDGINQV QCSVAEYPEA ITYLLEQYDR VEAEEARLSD LITGFVDPNA EEDLAPTATH 

       190        200        210        220        230        240 
VGSELSQEDL DDDEDEDEED GDDDSADDDN SIDPELAREK FAELRAQYVV TRDTIKAKGR 

       250        260        270        280        290        300 
SHATAQEEIL KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK 

       310        320        330        340        350        360 
NFITLFTGNE TSDTWFNAAI AMNKPWSEKL HDVSEEVHRA LQKLQQIEEE TGLTIEQVKD 

       370        380        390        400        410        420 
INRRMSIGEA KARRAKKEMV EANLRLVISI AKKYTNRGLQ FLDLIQEGNI GLMKAVDKFE 

       430        440        450        460        470        480 
YRRGYKFSTY ATWWIRQAIT RSIADQARTI RIPVHMIETI NKLNRISRQM LQEMGREPTP 

       490        500        510        520        530        540 
EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL 

       550        560        570        580        590        600 
RAATHDVLAG LTAREAKVLR MRFGIDMNTD YTLEEVGKQF DVTRERIRQI EAKALRKLRH 

       610 
PSRSEVLRSF LDD 

« Hide

References

« Hide 'large scale' references
[1]"The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12."
Burton Z.F., Burgess R.R., Lin J., Moore D., Holder S., Gross C.A.
Nucleic Acids Res. 9:2889-2903(1981) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: K12.
[2]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The subunits of DNA-dependent RNA polymerase from E. coli: I. Amino acid analysis and primary structure of the N-terminal regions."
Fujiki H., Zurek G.
FEBS Lett. 55:242-244(1975) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 1-4.
Strain: K12.
[5]"Promoter selectivity of Escherichia coli RNA polymerase. Purification and properties of holoenzyme containing the heat-shock sigma subunit."
Fujita N., Nomura T., Ishihama A.
J. Biol. Chem. 262:1855-1859(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
Strain: K12 / W3350 / ATCC 27020.
[6]"Growth phase-dependent modification of RNA polymerase in Escherichia coli."
Ozaki M., Wada A., Fujita N., Ishihama A.
Mol. Gen. Genet. 230:17-23(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[7]"Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA."
Dombroski A.J., Walter W.A., Record M.T. Jr., Siegele D.A., Gross C.A.
Cell 70:501-512(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DNA-BINDING, DOMAIN.
[8]"Role of the sigma 70 subunit of Escherichia coli RNA polymerase in transcription activation."
Kumar A., Grimes B., Fujita N., Makino K., Malloch R.A., Hayward R.S., Ishihama A.
J. Mol. Biol. 235:405-413(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[9]"Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions."
Jishage M., Iwata A., Ueda S., Ishihama A.
J. Bacteriol. 178:5447-5451(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
Strain: K12.
[10]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[11]"Interactions between activating region 3 of the Escherichia coli cyclic AMP receptor protein and region 4 of the RNA polymerase sigma(70) subunit: application of suppression genetics."
Rhodius V.A., Busby S.J.
J. Mol. Biol. 299:311-324(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: PROBABLE INTERACTION WITH CRP, MUTAGENESIS OF ARG-596.
[12]"In vitro transcription profiling of the sigmaS subunit of bacterial RNA polymerase: re-definition of the sigmaS regulon and identification of sigmaS-specific promoter sequence elements."
Maciag A., Peano C., Pietrelli A., Egli T., De Bellis G., Landini P.
Nucleic Acids Res. 39:5338-5355(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
Strain: K12 / MG1655 / ATCC 47076.
[13]"Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase."
Malhotra A., Severinova E., Darst S.A.
Cell 87:127-136(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 114-448.
[14]"T4 AsiA blocks DNA recognition by remodeling sigma70 region 4."
Lambert L.J., Wei Y., Schirf V., Demeler B., Werner M.H.
EMBO J. 23:2952-2962(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 533-613 IN COMPLEX WITH PHAGE T4 PROTEIN ASIA, SUBUNIT.
[15]"Crystal structure of the Escherichia coli regulator of sigma70, Rsd, in complex with sigma70 domain 4."
Patikoglou G.A., Westblade L.F., Campbell E.A., Lamour V., Lane W.J., Darst S.A.
J. Mol. Biol. 372:649-659(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 546-613 IN COMPLEX WITH RSD, SUBUNIT.
[16]"Three-dimensional EM structure of an intact activator-dependent transcription initiation complex."
Hudson B.P., Quispe J., Lara-Gonzalez S., Kim Y., Berman H.M., Arnold E., Ebright R.H., Lawson C.L.
Proc. Natl. Acad. Sci. U.S.A. 106:19830-19835(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY ELECTRON MICROSCOPY (19.80 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC; RPOZ; CRP AND DNA, DOMAIN, DNA-BINDING, SUBUNIT.
[17]"The structure of a transcription activation subcomplex reveals how sigma(70) is recruited to PhoB promoters."
Blanco A.G., Canals A., Bernues J., Sola M., Coll M.
EMBO J. 30:3776-3785(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (4.33 ANGSTROMS) OF 533-609 IN COMPLEX WITH RPOB; PHOB AND PHO BOX DNA, DNA-BINDING, SUBUNIT, DOMAIN.
[18]"X-ray crystal structure of Escherichia coli RNA polymerase sigma70 holoenzyme."
Murakami K.S.
J. Biol. Chem. 288:9126-9134(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.70 ANGSTROMS) IN COMPLEX WITH RPOA; RPOB; RPOC AND RPOZ, SUBUNIT.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J01687 Genomic DNA. Translation: AAA24601.1.
U28379 Genomic DNA. Translation: AAA89147.1.
U00096 Genomic DNA. Translation: AAC76103.1.
AP009048 Genomic DNA. Translation: BAE77118.1.
PIRRNECS. A65095.
RefSeqNP_417539.1. NC_000913.3.
YP_491259.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1SIGX-ray2.60A114-448[»]
1TLHNMR-B533-613[»]
2P7VX-ray2.60B546-613[»]
3IYDelectron microscopy19.8F1-613[»]
3T72X-ray4.33o/q533-609[»]
4IGCX-ray3.70X/Y1-613[»]
4JK1X-ray3.90X/Y1-613[»]
4JK2X-ray4.20X/Y1-613[»]
4JKRX-ray4.20F/L1-613[»]
4KMUX-ray3.85X/Y1-613[»]
4KN4X-ray3.96X/Y1-613[»]
4KN7X-ray3.69X/Y1-613[»]
4LJZX-ray3.59F/L92-613[»]
4LK0X-ray3.91F/L92-613[»]
4LK1X-ray3.84F/L1-613[»]
4LLGX-ray3.79F/L1-613[»]
ProteinModelPortalP00579.
SMRP00579. Positions 5-613.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10773N.
IntActP00579. 56 interactions.
MINTMINT-1220595.
STRING511145.b3067.

Chemistry

BindingDBP00579.

Proteomic databases

PaxDbP00579.
PRIDEP00579.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC76103; AAC76103; b3067.
BAE77118; BAE77118; BAE77118.
GeneID12932074.
947567.
KEGGecj:Y75_p2993.
eco:b3067.
PATRIC32121550. VBIEscCol129921_3162.

Organism-specific databases

EchoBASEEB0889.
EcoGeneEG10896. rpoD.

Phylogenomic databases

eggNOGCOG0568.
HOGENOMHOG000270272.
KOK03086.
OMAIEMNTDH.
OrthoDBEOG6XHC70.
PhylomeDBP00579.
ProtClustDBPRK05658.

Enzyme and pathway databases

BioCycEcoCyc:RPOD-MONOMER.
ECOL316407:JW3039-MONOMER.
MetaCyc:RPOD-MONOMER.

Gene expression databases

GenevestigatorP00579.

Family and domain databases

Gene3D1.10.10.10. 2 hits.
HAMAPMF_00963. Sigma70_RpoD_SigA.
InterProIPR014284. RNA_pol_sigma-70_dom.
IPR000943. RNA_pol_sigma70.
IPR009042. RNA_pol_sigma70_r1_2.
IPR007627. RNA_pol_sigma70_r2.
IPR007624. RNA_pol_sigma70_r3.
IPR007630. RNA_pol_sigma70_r4.
IPR007631. RNA_pol_sigma_70_non-ess.
IPR007127. RNA_pol_sigma_70_r1_1.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR028630. Sigma70_RpoD.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamPF04546. Sigma70_ner. 1 hit.
PF03979. Sigma70_r1_1. 1 hit.
PF00140. Sigma70_r1_2. 1 hit.
PF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]
PRINTSPR00046. SIGMA70FCT.
SUPFAMSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP00579.
PROP00579.

Entry information

Entry nameRPOD_ECOLI
AccessionPrimary (citable) accession number: P00579
Secondary accession number(s): Q2M9D8
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: October 1, 1996
Last modified: April 16, 2014
This is version 151 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene