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2 dna binding sequences of dna binding repressor

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Unformatted text preview: domains N-terminal domain = operator N-terminal binding binding C-terminal domain = C-terminal dimerization dimerization Lytic cycle initiated by Lytic cleavage of dimeric repressors in connector region region λ REPRESSOR - OPERATOR GEOMETRY REPRESSOR N-terminal N-terminal DNA binding domain domain C-terminal dimerization domain domain • • Weaver 2002 Molecular Biology Ed. 2 DNA-binding sequences of DNA-binding repressor exhibit a structure found repeatedly in DNAfound binding proteins from bacteria binding to eukaryotes: short stretches of α -helix N-terminal domain has 5 α N-terminal helices, two of which are used helices, to bind DNA and constitute the helix-turn-helix motif helix-turn-helix λ REPRESSOR - OPERATOR GEOMETRY REPRESSOR • helix turn helix α -helices 2 & 3 in each -helices subunit form H-bonds with operator DNA; in dimer, two helix-3 regions lie 34Å apart & fit into successive DNA major grooves on same side of helix same • α -helix 3 = RECOGNITION HELIX: it recognizes HELIX: specific target sequence specific • helix-turn-helix found in helix-turn-helix other DNA-binding proteins • one can change the DNAbinding specificity of a binding repressor by substituting its recognition helix with that from a different repressor repressor HYDROGEN BONDS BETWEEN λ REPRESSOR & OPERATOR DNA REPRESSOR OL1 Weaver 2002 Molecular Biology Ed. 2 • • • Cl & Cro are both helix-turn-helix repressors In both CI & Cro, 2 helix-3 amino acids are conserved (neighbouring In helix-3 Gln & Ser) that bond to specific bp in DNA Gln Helix-2 mediates H-bonding with phosphate backbone (for example Gln 33 in λ repressor) but doesn’t control specificity of target Gln ’t HYDROGEN BONDS BETWEEN λ REPRESSOR & OPERATOR DNA REPRESSOR OL1 Weaver 2002 Molecular Biology Ed. 2 • in addition to hydrogen bonding, helix-2 undergoes ionic in interactions with phosphate backbone due to fact that its amino end, which has a net positive charge, is pointing directly towards negatively charged DNA backbone directly OPERATOR/REPRESSOR-BINDING SITES: COOPERATIVE BINDING SITES: • • • -Repressor highest affinity for OL1 & OR1 Repressor R1 -Cooperative binding: binding at site 1 Cooperative increases repressor affinity for site 2; when OL1-2 & OR1-2 bound by repressor, PL & R1-2 PR transcription blocked • each operator contains each three 17bp repressorthree binding sites wit...
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