Solution structure of domain 1.1 of the σA factor from Bacillus subtilis is preformed for binding to the RNA polymerase core
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu srovnávací studie, časopisecké články, práce podpořená grantem
PubMed
28539362
PubMed Central
PMC5512058
DOI
10.1074/jbc.m117.784074
PII: S0021-9258(20)37029-0
Knihovny.cz E-zdroje
- Klíčová slova
- Bacillus, RNA polymerase, molecular modeling, nuclear magnetic resonance (NMR), protein structure, transcription initiation factor,
- MeSH
- Bacillus subtilis metabolismus MeSH
- bakteriální proteiny chemie genetika metabolismus MeSH
- DNA bakterií chemie metabolismus MeSH
- DNA řízené RNA-polymerasy chemie genetika metabolismus MeSH
- interakční proteinové domény a motivy MeSH
- izotopy dusíku MeSH
- izotopy uhlíku MeSH
- konformace nukleové kyseliny MeSH
- konformace proteinů MeSH
- konzervovaná sekvence MeSH
- molekulární modely * MeSH
- peptidové fragmenty chemie genetika metabolismus MeSH
- podjednotky proteinů MeSH
- rekombinantní proteiny chemie metabolismus MeSH
- sbalování proteinů MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- sigma faktor chemie genetika metabolismus MeSH
- stabilita proteinů MeSH
- strukturní homologie proteinů MeSH
- Thermotoga maritima enzymologie MeSH
- vazebná místa MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- srovnávací studie MeSH
- Názvy látek
- bakteriální proteiny MeSH
- DNA bakterií MeSH
- DNA řízené RNA-polymerasy MeSH
- izotopy dusíku MeSH
- izotopy uhlíku MeSH
- peptidové fragmenty MeSH
- podjednotky proteinů MeSH
- rekombinantní proteiny MeSH
- sigma faktor MeSH
Bacterial RNA polymerase (RNAP) requires σ factors to recognize promoter sequences. Domain 1.1 of primary σ factors (σ1.1) prevents their binding to promoter DNA in the absence of RNAP, and when in complex with RNAP, it occupies the DNA-binding channel of RNAP. Currently, two 3D structures of σ1.1 are available: from Escherichia coli in complex with RNAP and from T. maritima solved free in solution. However, these two structures significantly differ, and it is unclear whether this difference is due to an altered conformation upon RNAP binding or to differences in intrinsic properties between the proteins from these two distantly related species. Here, we report the solution structure of σ1.1 from the Gram-positive bacterium Bacillus subtilis We found that B. subtilis σ1.1 is highly compact because of additional stabilization not present in σ1.1 from the other two species and that it is more similar to E. coli σ1.1. Moreover, modeling studies suggested that B. subtilis σ1.1 requires minimal conformational changes for accommodating RNAP in the DNA channel, whereas T. maritima σ1.1 must be rearranged to fit therein. Thus, the mesophilic species B. subtilis and E. coli share the same σ1.1 fold, whereas the fold of σ1.1 from the thermophile T. maritima is distinctly different. Finally, we describe an intriguing similarity between σ1.1 and δ, an RNAP-associated protein in B. subtilis, bearing implications for the so-far unknown binding site of δ on RNAP. In conclusion, our results shed light on the conformational changes of σ1.1 required for its accommodation within bacterial RNAP.
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PDB
4LK1, 4YLN, 5MWW