Operator sequence of DNA

Ha et al. [18] have measured the equilibrium quotients for the formation of a complex between the lac repressor protein and a symmetric operator sequence of DNA as a function of temperature. Their results are given below. (The standard state is 1 mol dm. )... 

Oncogenic viruses 248 One-start helix 334 Oparin, I. V. 9 Open systems 289 Operator sequence of DNA iH NMR spectrum 269 Operons 240 Opsin(s) 553 Optical rotation 42 Optimum rate for enzymes 469 d Orbitals, participation in covalent bond formation 311 Orcinol 251 Ordered binding 464 Ordered sequential mechanism 475 Organelle(s) 11... 

Fig. 1.15. Bending of the DNA in the CAP protein-DNA complex. The CAP protein ( . coli) binds as a dimer to the two-fold symmetric operator sequence. The DNA is bent nearly 90deg in the complex. The turns are centered around two GT sequences (shown in black) of the recognition element.

Fig. 1.19. Tetramerization of the Lac repressor and loop formation of the DNA. The Lac repressor from E. coli binds as a dimer to the two-fold symmetric operator seqnence, whereby each of the monomers contacts a half-site of a recognition sequence. The Lac operon of E. coli possesses three operator sequences Of, 02 and 03, aU three of which are required for complete repression. Of and 03 are separated by 93 bp, and only these two sequences are displayed in the figure above. Between Of and 03 is a binding site for the CAP protein and the contact surface for the RNA polymerase. The Lac repressor acts as a tetramer. It is therefore assumed that two dimers of the repressor associate to form the active tetramer, whereby one of the two dimers is bound to 03, the other dimer binds to Of. The intervening DNA forms a so-caUed repression loop. After Lewis et al., 1996.

Historically, attenuation was discovered when it was noticed that deletion of a short sequence of DNA between the operator and the first structural gene, trpE, increased the level of transcription. This region was named the attenuator (see Fig. 1) and is the DNA that encodes that part of the leader sequence that forms the transcription terminator stem-loop. 

Figure 3.7 The crystal structure of DtxR, a 226-residue three-domain dimeric protein, is shown. The protein, activated by cobalt (designated 1 and 2), is bound to a 21-bp DNA duplex based on the consensus operator sequence. Two DtxR dimers surround the DNA duplex, which is distorted compared to canonical B-DNA. Only domain 1, involved in DNA-binding, and domain 2, involved in dimer formation, are shown. The helices of the DNA-binding domain are indicated by HI, H2, and H3. H3 binds to the major groove of the DNA. From Pohl et al., 1999, by permission of Academic Press. 

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