RNA polymerase sigma factor RpoD - P00579 (RPOD_ECOLI)


Protein Feature View of PDB entries mapped to a UniProtKB sequence  

  • Number of PDB entries for P00579: 23
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. (data source: UniProt  )
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. (data source: UniProt  )
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). (data source: UniProt  )
Other Gene names: rpoD alt b3067 JW3039
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Data in green originates from UniProtKB  
Data in yellow originates from Pfam  , by interacting with the HMMER3 web site  
Data in purple originates from Phosphosite  .
Data in orange originates from the SCOP   (version 1.75) and SCOPe   (version 2.04) classifications.
Data in grey has been calculated using BioJava  . Protein disorder predictions are based on JRONN (Troshin, P. and Barton, G. J. unpublished), a Java implementation of RONN  
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  • Blue: hydrophilic.
Data in lilac represent the genomic exon structure projected onto the UniProt sequence.
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  • Secstruc: Secondary structure projected from representative PDB entries onto the UniProt sequence.
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The PDB to UniProt mapping is based on the data provided by the EBI SIFTS project. See also Velankar et al., Nucleic Acids Research 33, D262-265 (2005).
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