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#promoter elements

2 public questions tagged with this topic.

TATA box is usually located at

In canonical Pol II promoters, TATA box is located twenty-five to thirty-five base pairs upstream of transcription start site, typically centered near minus thirty, at precise distance to align polymerase active site with initiator. This spacing is critical because TBP bending orients TFIIB N-terminal ribbon to contact polymerase and to direct opening of DNA downstream. Prokaryotic minus ten Pribnow box functionally analogous to TATA. Promoters lacking TATA utilize downstream promoter element DPE or initiator Inr to recruit TFIID via TAF subunits at alternative positions.

Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 10: TATA box location -30; Berg et al., Biochemistry, Promoter mapping and spacing

Which subunit recognizes the -10 and -35 promoter elements?

Within bacterial holoenzyme, sequence-specific readout of promoter consensus relies predominantly on sigma factor rather than core catalytic subunits. Sigma70 region 4.2 presents helix-turn-helix motif inserting into major groove at -35 element TTGACA, while region 2.4 interacts with -10 Pribnow box TATAAT and captures flipped bases to drive melting. α subunit C-terminal domain may touch UP element AT-rich tract, but -10 and -35 recognition is sigma intrinsic. β and β' subunits shape downstream DNA channel and catalytic Mg2+ but do not determine promoter consensus identity. Exchange of sigma alters promoter preference accordingly.

Ref: Alberts Molecular Biology Cell Chapter 6: Sigma subunit recognizes -10 -35 elements; Watson Chapter 13 Sigma-DNA contacts