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Feature IC3 (early initiation) EC (elongation) IC7 Biochemical features Promoter bound released like IC3 Bubble expanding on downstream side closing upstream, opening downstream like IC3 DNA RNA hybrid 3 bp 7-8 bp 7 bp 5'-end of RNA part of hybrid single stranded like IC3 RNA release frequent none like IC3 Structural features Structural representatives 1QLN 1MSW, 1H38 3E2E Promoter binding site intact destroyed like IC3 RNA exit channel blocked formed like IC3 Preventing upstream bubble collapse protein RNA like IC3 Interactions between helix C and C-terminal domain present present present Thumb helix bound to PBD bound to hybrid like EC Table 1. Biochemical and structural features of different stages in transcription
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Residue involved in RNA binding in the EC* Nucleotide interaction partner** Role in IC7 Role in IC3 K441 (-1, -2) RNA interaction RNA interaction R425 -2 RNA interaction RNA interaction R394 -4 RNA interaction RNA interaction K389 -5 RNA interaction bound to PBD R386 (-5, -6) RNA interaction RNA interaction K172 (-5, -6) distant from RNA (part of sub domain H) distant from RNA (part of sub domain H) R756*** ~ -9 Promoter binding Promoter binding R746*** ~ -9 Promoter binding Promoter binding *interactions of positively charged residues according to Tahirov et al. (2002); **numbering relative to the active site, not the transcription start site; ***based on 1MSW coordinates (Yin and Steitz, 2002). Table 2. Protein RNA interactions in transcription complexes
Figure 4 个
Table 2 个
