DNA-dependent RNA polymerase / tagetitoxin complex
Thermus thermophilus (thermophile, bacteria)
RNA polymerase (RNAP) plays a central role in gene expression, and is a target of many kinds of regulatory proteins and small-molecule effectors. The enzymatic reaction of RNAP is mainly nucleotide addition. RNAP transfers the nucleotidyl moiety of NTP (nucleoside triphosphate) coming from the secondary channel to the 3’-OH of the nascent RNA, and chops off pyrophosphate (PPi), and then creates new space for the NTP coming next by enzyme translocation. This series of reactions is supposed to be mediated by two catalytic Mg2+ ions near the active site. Tagetitoxin (Tgt) is one type of phytotoxin produced by a certain kind of mold. Tgt inhibits transcription by RNAP in chloroplasts by an unknown mechanism, and causes apical chlorosis in infected plants.
The structure shown here is of the complex of Tgt and RNAP from Thermus thermophilus. This RNAP consists of a five-subunit core (alpha, alpha, beta, beta’, omega) and sigma factor rpoD. 9 of 11 Tgt oxygen atoms form 18 hydrogen bonds with highly conserved basic residues on the beta and beta’ chains, so binding of Tgt to RNAP is mediated exclusively by polar interactions. A well-fixed Mg2+ ion (tMg) is located midway between Tgt and Asp460, and two more catalytic Mg2+ ions are in the vicinity. The authors suggest that tMG binds and stabilizes NTP-bound intermediate and inhibits the release of PPi, thus halting nucleotide addition. This structure includes two sets of complex with RNAP, sigma factor rpoD, Tgt and so on. The one set structure is shown in fig. 1.
Fig.1. The structure of RNAP complexed with sigma factor (rpoD), Tgt, and so on.
Protein Data Bank (PDB)
author: Miho Higurashi