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Protein

RNA polymerase sigma factor RpoD

Gene

rpoD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.UniRule annotation6 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi573 – 592H-T-H motifUniRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Sigma factor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

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

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor RpoDUniRule annotation
Alternative name(s):
Sigma-70UniRule annotation
Gene namesi
Name:rpoDUniRule annotation
Synonyms:alt
Ordered Locus Names:b3067, JW3039
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10896. rpoD.

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi596R → D or E: 2-fold reduction in activation of class II Crp-dependent promoters. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000938851 – 613RNA polymerase sigma factor RpoDAdd BLAST613

Proteomic databases

EPDiP00579.
PaxDbiP00579.
PRIDEiP00579.

Interactioni

Subunit structurei

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.UniRule annotation5 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei562Interaction with anti-sigma factors1

Binary interactionsi

WithEntry#Exp.IntActNotes
asiAP322675EBI-545104,EBI-2124737From a different organism.
rpoCP0A8T78EBI-545104,EBI-543604
rsdP0AFX411EBI-545104,EBI-1134364

Protein-protein interaction databases

BioGridi4261068. 180 interactors.
DIPiDIP-10773N.
IntActiP00579. 56 interactors.
MINTiMINT-1220595.
STRINGi511145.b3067.

Structurei

Secondary structure

1613
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi116 – 134Combined sources19
Helixi138 – 148Combined sources11
Turni149 – 154Combined sources6
Helixi158 – 160Combined sources3
Beta strandi162 – 165Combined sources4
Turni179 – 182Combined sources4
Turni187 – 190Combined sources4
Helixi214 – 234Combined sources21
Helixi243 – 256Combined sources14
Beta strandi259 – 261Combined sources3
Helixi263 – 292Combined sources30
Helixi299 – 306Combined sources8
Turni307 – 309Combined sources3
Helixi313 – 315Combined sources3
Helixi317 – 320Combined sources4
Helixi325 – 329Combined sources5
Helixi330 – 332Combined sources3
Helixi334 – 351Combined sources18
Helixi355 – 382Combined sources28
Helixi384 – 391Combined sources8
Beta strandi397 – 399Combined sources3
Helixi401 – 418Combined sources18
Helixi421 – 423Combined sources3
Helixi427 – 445Combined sources19
Turni547 – 550Combined sources4
Helixi553 – 562Combined sources10
Helixi573 – 597Combined sources25

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SIGX-ray2.60A114-448[»]
1TLHNMR-B533-613[»]
2P7VX-ray2.60B546-613[»]
3IYDelectron microscopy19.8F1-613[»]
3T72X-ray4.33o/q533-609[»]
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[»]
4MEXX-ray3.90F/L1-613[»]
4MEYX-ray3.95F/L1-613[»]
4XSXX-ray3.71F/L92-613[»]
4XSYX-ray4.01F/L92-613[»]
4XSZX-ray3.68F/L92-613[»]
4YFKX-ray3.57F/L1-613[»]
4YFNX-ray3.82F/L1-613[»]
4YFXX-ray3.84F/L1-613[»]
4YG2X-ray3.70F/L1-613[»]
4YLNX-ray5.50F/L/R1-613[»]
4YLOX-ray6.00F/L/R1-613[»]
4YLPX-ray5.50F/L/R1-613[»]
4ZH2X-ray4.20F/L1-613[»]
4ZH3X-ray4.08F/L1-613[»]
4ZH4X-ray3.99F/L1-613[»]
ProteinModelPortaliP00579.
SMRiP00579.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP00579.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 80Sigma-70 factor domain-1Add BLAST79
Regioni379 – 449Sigma-70 factor domain-2Add BLAST71
Regioni458 – 534Sigma-70 factor domain-3Add BLAST77
Regioni547 – 600Sigma-70 factor domain-4Add BLAST54
Regioni584 – 599Interaction with anti-sigma factorsAdd BLAST16

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi403 – 406Interaction with polymerase core subunit RpoC4

Domaini

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.Curated
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.
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 (PubMed:19903881 and PubMed:21829166). This domain is probably also responsible for interaction with Crp (PubMed:10860740).1 Publication

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270272.
InParanoidiP00579.
KOiK03086.
OMAiRDAKKEM.
PhylomeDBiP00579.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 1 hit.
InterProiIPR014284. 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]
PfamiPF04546. 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]
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P00579-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND
60 70 80 90 100
MGIQVMEEAP DADDLMLAEN TADEDAAEAA AQVLSSVESE IGRTTDPVRM
110 120 130 140 150
YMREMGTVEL LTREGEIDIA KRIEDGINQV QCSVAEYPEA ITYLLEQYDR
160 170 180 190 200
VEAEEARLSD LITGFVDPNA EEDLAPTATH VGSELSQEDL DDDEDEDEED
210 220 230 240 250
GDDDSADDDN SIDPELAREK FAELRAQYVV TRDTIKAKGR SHATAQEEIL
260 270 280 290 300
KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK
310 320 330 340 350
NFITLFTGNE TSDTWFNAAI AMNKPWSEKL HDVSEEVHRA LQKLQQIEEE
360 370 380 390 400
TGLTIEQVKD INRRMSIGEA KARRAKKEMV EANLRLVISI AKKYTNRGLQ
410 420 430 440 450
FLDLIQEGNI GLMKAVDKFE YRRGYKFSTY ATWWIRQAIT RSIADQARTI
460 470 480 490 500
RIPVHMIETI NKLNRISRQM LQEMGREPTP EELAERMLMP EDKIRKVLKI
510 520 530 540 550
AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL RAATHDVLAG
560 570 580 590 600
LTAREAKVLR MRFGIDMNTD YTLEEVGKQF DVTRERIRQI EAKALRKLRH
610
PSRSEVLRSF LDD
Length:613
Mass (Da):70,263
Last modified:October 1, 1996 - v2
Checksum:iCA4F0E30DEC1703D
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti149D → N in AAA24601 (PubMed:6269063).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01687 Genomic DNA. Translation: AAA24601.1.
U28379 Genomic DNA. Translation: AAA89147.1.
U00096 Genomic DNA. Translation: AAC76103.1.
AP009048 Genomic DNA. Translation: BAE77118.1.
PIRiA65095. RNECS.
RefSeqiNP_417539.1. NC_000913.3.
WP_000437376.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76103; AAC76103; b3067.
BAE77118; BAE77118; BAE77118.
GeneIDi947567.
KEGGiecj:JW3039.
eco:b3067.
PATRICi32121550. VBIEscCol129921_3162.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J01687 Genomic DNA. Translation: AAA24601.1.
U28379 Genomic DNA. Translation: AAA89147.1.
U00096 Genomic DNA. Translation: AAC76103.1.
AP009048 Genomic DNA. Translation: BAE77118.1.
PIRiA65095. RNECS.
RefSeqiNP_417539.1. NC_000913.3.
WP_000437376.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1SIGX-ray2.60A114-448[»]
1TLHNMR-B533-613[»]
2P7VX-ray2.60B546-613[»]
3IYDelectron microscopy19.8F1-613[»]
3T72X-ray4.33o/q533-609[»]
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[»]
4MEXX-ray3.90F/L1-613[»]
4MEYX-ray3.95F/L1-613[»]
4XSXX-ray3.71F/L92-613[»]
4XSYX-ray4.01F/L92-613[»]
4XSZX-ray3.68F/L92-613[»]
4YFKX-ray3.57F/L1-613[»]
4YFNX-ray3.82F/L1-613[»]
4YFXX-ray3.84F/L1-613[»]
4YG2X-ray3.70F/L1-613[»]
4YLNX-ray5.50F/L/R1-613[»]
4YLOX-ray6.00F/L/R1-613[»]
4YLPX-ray5.50F/L/R1-613[»]
4ZH2X-ray4.20F/L1-613[»]
4ZH3X-ray4.08F/L1-613[»]
4ZH4X-ray3.99F/L1-613[»]
ProteinModelPortaliP00579.
SMRiP00579.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261068. 180 interactors.
DIPiDIP-10773N.
IntActiP00579. 56 interactors.
MINTiMINT-1220595.
STRINGi511145.b3067.

Proteomic databases

EPDiP00579.
PaxDbiP00579.
PRIDEiP00579.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76103; AAC76103; b3067.
BAE77118; BAE77118; BAE77118.
GeneIDi947567.
KEGGiecj:JW3039.
eco:b3067.
PATRICi32121550. VBIEscCol129921_3162.

Organism-specific databases

EchoBASEiEB0889.
EcoGeneiEG10896. rpoD.

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270272.
InParanoidiP00579.
KOiK03086.
OMAiRDAKKEM.
PhylomeDBiP00579.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP00579.
PROiP00579.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 1 hit.
InterProiIPR014284. 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]
PfamiPF04546. 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]
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPOD_ECOLI
AccessioniPrimary (citable) accession number: P00579
Secondary accession number(s): Q2M9D8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: October 1, 1996
Last modified: November 2, 2016
This is version 170 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.