UniProtKB - P00579 (RPOD_ECOLI)
RNA polymerase sigma factor RpoD
rpoD
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 annotation7 PublicationsRegions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
DNA bindingi | 573 – 592 | H-T-H motifUniRule annotationAdd BLAST | 20 |
GO - Molecular functioni
- DNA binding Source: UniProtKB-UniRule
- sigma factor activity Source: EcoliWiki
GO - Biological processi
- DNA-templated transcription, initiation Source: InterPro
- regulation of DNA-templated transcription, initiation Source: ComplexPortal
- response to heat Source: EcoliWiki
Keywordsi
Molecular function | DNA-binding, Sigma factor |
Biological process | Transcription, Transcription regulation |
Enzyme and pathway databases
BioCyci | EcoCyc:RPOD-MONOMER |
Names & Taxonomyi
Protein namesi | Recommended name: RNA polymerase sigma factor RpoDUniRule annotationAlternative name(s): Sigma-70UniRule annotation |
Gene namesi | Name:rpoDUniRule annotation Synonyms:alt Ordered Locus Names:b3067, JW3039 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
Cytoplasm and Cytosol
- Cytoplasm UniRule annotation
Cytosol
- cytosol Source: EcoCyc
- cytosolic DNA-directed RNA polymerase complex Source: ComplexPortal
Other locations
- sigma factor antagonist complex Source: ComplexPortal
Keywords - Cellular componenti
CytoplasmPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 553 | A → D: Disrupts the interaction with Escherichia phage lambda antitermination protein Q. 1 Publication | 1 | |
Mutagenesisi | 596 | R → D or E: 2-fold reduction in activation of class II Crp-dependent promoters. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000093885 | 1 – 613 | RNA polymerase sigma factor RpoDAdd BLAST | 613 |
Proteomic databases
jPOSTi | P00579 |
PaxDbi | P00579 |
PRIDEi | P00579 |
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 annotation6 Publications(Microbial infection) Interacts with Escherichia phage lambda antitermination protein Q.
1 PublicationSites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sitei | 562 | Interaction with anti-sigma factors | 1 |
Binary interactionsi
P00579
With | #Exp. | IntAct |
---|---|---|
rpoB [P0A8V2] | 10 | EBI-545104,EBI-544996 |
rpoC [P0A8T7] | 11 | EBI-545104,EBI-543604 |
rsd [P0AFX4] | 11 | EBI-545104,EBI-1134364 |
asiA [P32267] from Enterobacteria phage T4. | 7 | EBI-545104,EBI-2124737 |
Protein-protein interaction databases
BioGRIDi | 4261068, 200 interactors 851883, 14 interactors |
ComplexPortali | CPX-4881, DNA-directed RNA polymerase holoenzyme complex, Sigma70 variant CPX-4901, rpod-rsd sigma-antisigma complex |
DIPi | DIP-10773N |
IntActi | P00579, 56 interactors |
STRINGi | 511145.b3067 |
Structurei
Secondary structure
3D structure databases
BMRBi | P00579 |
SMRi | P00579 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P00579 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 2 – 80 | Sigma-70 factor domain-1Add BLAST | 79 | |
Regioni | 176 – 213 | DisorderedSequence analysisAdd BLAST | 38 | |
Regioni | 379 – 449 | Sigma-70 factor domain-2Add BLAST | 71 | |
Regioni | 458 – 534 | Sigma-70 factor domain-3Add BLAST | 77 | |
Regioni | 547 – 600 | Sigma-70 factor domain-4Add BLAST | 54 | |
Regioni | 584 – 599 | Interaction with anti-sigma factorsAdd BLAST | 16 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 403 – 406 | Interaction with polymerase core subunit RpoC | 4 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 187 – 210 | Acidic residuesSequence analysisAdd BLAST | 24 |
Domaini
Sequence similaritiesi
Phylogenomic databases
eggNOGi | COG0568, Bacteria |
HOGENOMi | CLU_014793_7_2_6 |
InParanoidi | P00579 |
PhylomeDBi | P00579 |
Family and domain databases
Gene3Di | 1.10.10.10, 2 hits 1.10.220.120, 1 hit |
HAMAPi | MF_00963, Sigma70_RpoD_SigA, 1 hit |
InterProi | View protein in InterPro IPR014284, 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 IPR042189, RNA_pol_sigma_70_r1_1_sf IPR013325, RNA_pol_sigma_r2 IPR013324, RNA_pol_sigma_r3/r4-like IPR012760, RNA_pol_sigma_RpoD_C IPR028630, Sigma70_RpoD IPR036388, WH-like_DNA-bd_sf |
Pfami | View protein in Pfam PF04546, 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 |
PRINTSi | PR00046, SIGMA70FCT |
SUPFAMi | SSF88659, SSF88659, 2 hits SSF88946, SSF88946, 1 hit |
TIGRFAMsi | TIGR02393, RpoD_Cterm, 1 hit TIGR02937, sigma70-ECF, 1 hit |
PROSITEi | View protein in PROSITE PS00715, SIGMA70_1, 1 hit PS00716, SIGMA70_2, 1 hit |
i Sequence
Sequence statusi: Complete.
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 149 | D → N in AAA24601 (PubMed:6269063).Curated | 1 |
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 |
PIRi | A65095, RNECS |
RefSeqi | NP_417539.1, NC_000913.3 WP_000437376.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC76103; AAC76103; b3067 BAE77118; BAE77118; BAE77118 |
GeneIDi | 947567 |
KEGGi | ecj:JW3039 eco:b3067 |
PATRICi | fig|1411691.4.peg.3662 |
Similar proteinsi
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 |
PIRi | A65095, RNECS |
RefSeqi | NP_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 entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
1SIG | X-ray | 2.60 | A | 114-448 | [»] | |
1TLH | NMR | - | B | 533-613 | [»] | |
2P7V | X-ray | 2.60 | B | 546-613 | [»] | |
3IYD | electron microscopy | 19.80 | F | 1-613 | [»] | |
3T72 | X-ray | 4.33 | o/q | 533-609 | [»] | |
4JK1 | X-ray | 3.90 | X/Y | 1-613 | [»] | |
4JK2 | X-ray | 4.20 | X/Y | 1-613 | [»] | |
4JKR | X-ray | 4.20 | F/L | 1-613 | [»] | |
4KMU | X-ray | 3.85 | X/Y | 1-613 | [»] | |
4KN4 | X-ray | 3.96 | X/Y | 1-613 | [»] | |
4KN7 | X-ray | 3.69 | X/Y | 1-613 | [»] | |
4LJZ | X-ray | 3.59 | F/L | 92-613 | [»] | |
4LK0 | X-ray | 3.91 | F/L | 92-613 | [»] | |
4LK1 | X-ray | 3.84 | F/L | 1-613 | [»] | |
4LLG | X-ray | 3.79 | F/L | 1-613 | [»] | |
4MEX | X-ray | 3.90 | F/L | 1-613 | [»] | |
4MEY | X-ray | 3.95 | F/L | 1-613 | [»] | |
4XSX | X-ray | 3.71 | F/L | 92-613 | [»] | |
4XSY | X-ray | 4.01 | F/L | 92-613 | [»] | |
4XSZ | X-ray | 3.68 | F/L | 92-613 | [»] | |
4YFK | X-ray | 3.57 | F/L | 1-613 | [»] | |
4YFN | X-ray | 3.82 | F/L | 1-613 | [»] | |
4YFX | X-ray | 3.84 | F/L | 1-613 | [»] | |
4YG2 | X-ray | 3.70 | F/L | 1-613 | [»] | |
4YLN | X-ray | 5.50 | F/L/R | 1-613 | [»] | |
4YLO | X-ray | 6.00 | F/L/R | 1-613 | [»] | |
4YLP | X-ray | 5.50 | F/L/R | 1-613 | [»] | |
4ZH2 | X-ray | 4.20 | F/L | 1-613 | [»] | |
4ZH3 | X-ray | 4.08 | F/L | 1-613 | [»] | |
4ZH4 | X-ray | 3.99 | F/L | 1-613 | [»] | |
5UAC | X-ray | 3.80 | F/L | 1-613 | [»] | |
5UAG | X-ray | 3.40 | F/L | 1-613 | [»] | |
5UAH | X-ray | 4.10 | F/L | 1-613 | [»] | |
5UAJ | X-ray | 3.92 | F/L | 1-613 | [»] | |
5UAL | X-ray | 3.89 | F/L | 1-613 | [»] | |
5UAQ | X-ray | 3.60 | F/L | 1-613 | [»] | |
5VSW | X-ray | 4.29 | F/L | 1-613 | [»] | |
5VT0 | electron microscopy | 3.78 | L | 94-613 | [»] | |
5W1S | X-ray | 3.81 | F/L | 1-613 | [»] | |
5W1T | X-ray | 4.50 | F/L | 1-613 | [»] | |
6B6H | electron microscopy | 3.90 | F | 1-613 | [»] | |
6BYU | X-ray | 3.60 | F/L | 1-613 | [»] | |
6C9Y | electron microscopy | 4.25 | F | 1-613 | [»] | |
6CA0 | electron microscopy | 5.75 | F | 1-613 | [»] | |
6CUX | X-ray | 4.10 | F/L | 1-613 | [»] | |
6JNX | electron microscopy | 4.08 | F | 1-613 | [»] | |
6K4Y | electron microscopy | 3.79 | F | 1-613 | [»] | |
6LDI | electron microscopy | 3.69 | F | 1-613 | [»] | |
6N4C | electron microscopy | 17.00 | F | 8-613 | [»] | |
6N57 | electron microscopy | 3.70 | L | 1-613 | [»] | |
6N58 | electron microscopy | 3.78 | L | 1-613 | [»] | |
6OUL | electron microscopy | 3.40 | L | 1-613 | [»] | |
6P18 | electron microscopy | 3.50 | F | 1-613 | [»] | |
6P1K | electron microscopy | 4.05 | L | 1-613 | [»] | |
6PB4 | electron microscopy | 4.35 | F | 1-613 | [»] | |
6PB5 | electron microscopy | 4.52 | F | 1-613 | [»] | |
6PB6 | electron microscopy | 4.29 | F | 1-613 | [»] | |
6PSQ | electron microscopy | 3.40 | L | 1-613 | [»] | |
6PSR | electron microscopy | 3.40 | L | 1-613 | [»] | |
6PSS | electron microscopy | 3.50 | L | 1-613 | [»] | |
6PST | electron microscopy | 3.00 | L | 1-613 | [»] | |
6PSU | electron microscopy | 3.90 | L | 1-613 | [»] | |
6PSV | electron microscopy | 3.50 | L | 1-613 | [»] | |
6PSW | electron microscopy | 3.70 | L | 1-613 | [»] | |
6VJS | X-ray | 4.02 | X/Y | 1-613 | [»] | |
6XH7 | electron microscopy | 3.90 | F | 1-613 | [»] | |
6XH8 | electron microscopy | 4.10 | F | 1-613 | [»] | |
6XL5 | electron microscopy | 2.50 | F | 1-613 | [»] | |
6XL9 | electron microscopy | 2.50 | F | 1-613 | [»] | |
6XLJ | electron microscopy | 2.70 | F | 1-613 | [»] | |
6XLL | electron microscopy | 2.70 | F | 1-613 | [»] | |
6XLM | electron microscopy | 3.20 | F | 1-613 | [»] | |
7C17 | electron microscopy | 4.22 | F | 1-613 | [»] | |
7C97 | electron microscopy | 3.68 | F | 1-613 | [»] | |
7CHW | electron microscopy | 3.58 | F | 1-613 | [»] | |
7KHB | electron microscopy | 3.53 | F | 1-613 | [»] | |
7KHC | electron microscopy | 4.14 | F | 1-613 | [»] | |
7KHE | electron microscopy | 3.58 | F | 1-613 | [»] | |
7KHI | electron microscopy | 3.62 | F | 1-613 | [»] | |
BMRBi | P00579 | |||||
SMRi | P00579 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4261068, 200 interactors 851883, 14 interactors |
ComplexPortali | CPX-4881, DNA-directed RNA polymerase holoenzyme complex, Sigma70 variant CPX-4901, rpod-rsd sigma-antisigma complex |
DIPi | DIP-10773N |
IntActi | P00579, 56 interactors |
STRINGi | 511145.b3067 |
Proteomic databases
jPOSTi | P00579 |
PaxDbi | P00579 |
PRIDEi | P00579 |
Genome annotation databases
EnsemblBacteriai | AAC76103; AAC76103; b3067 BAE77118; BAE77118; BAE77118 |
GeneIDi | 947567 |
KEGGi | ecj:JW3039 eco:b3067 |
PATRICi | fig|1411691.4.peg.3662 |
Organism-specific databases
EchoBASEi | EB0889 |
Phylogenomic databases
eggNOGi | COG0568, Bacteria |
HOGENOMi | CLU_014793_7_2_6 |
InParanoidi | P00579 |
PhylomeDBi | P00579 |
Enzyme and pathway databases
BioCyci | EcoCyc:RPOD-MONOMER |
Miscellaneous databases
EvolutionaryTracei | P00579 |
PROi | PR:P00579 |
Family and domain databases
Gene3Di | 1.10.10.10, 2 hits 1.10.220.120, 1 hit |
HAMAPi | MF_00963, Sigma70_RpoD_SigA, 1 hit |
InterProi | View protein in InterPro IPR014284, 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 IPR042189, RNA_pol_sigma_70_r1_1_sf IPR013325, RNA_pol_sigma_r2 IPR013324, RNA_pol_sigma_r3/r4-like IPR012760, RNA_pol_sigma_RpoD_C IPR028630, Sigma70_RpoD IPR036388, WH-like_DNA-bd_sf |
Pfami | View protein in Pfam PF04546, 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 |
PRINTSi | PR00046, SIGMA70FCT |
SUPFAMi | SSF88659, SSF88659, 2 hits SSF88946, SSF88946, 1 hit |
TIGRFAMsi | TIGR02393, RpoD_Cterm, 1 hit TIGR02937, sigma70-ECF, 1 hit |
PROSITEi | View protein in PROSITE PS00715, SIGMA70_1, 1 hit PS00716, SIGMA70_2, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | RPOD_ECOLI | |
Accessioni | P00579Primary (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: | February 23, 2022 | |
This is version 207 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families