Lambda repressor: Difference between revisions

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==Structural Overview==
==Structural Overview==
The Lambda Repressor dimer is composed of two identical polypeptide chains of 236 amino acid residues each.  The dimer is formed mainly by interactions between the CTDs, while the NTDs interact weakly in comparison.  Each chain is composed of two structurally distinct domains which are connected by a short polypeptide chain which contains a cleavage-sensitive region (CSR).  The NTD is responsible for the DNA-binding character of the protein and the CTD is integral in dimerization of the chains, cooperative-binding repression, and the auto-cleavage mechanism ().  The principal purpose of the CSR is to provide a region which is both susceptible and insusceptible to cleavage depending upon the conformation the dimer assumes.  In addition, the CSR serves to stabilize interactions between chains in the dimer.
The Lambda Repressor <scene name='Bacteriophage_Lambda_Repressor_cI/Homodimer_bound_to_dna/3'>homodimer</scene> is composed of two identical polypeptide chains of 236 amino acid residues each.  The dimer is formed mainly by interactions between the C-Terminal domains (CTDs) of two monomers, while the N-Terminal domains (NTDs) interact weakly in comparison.  Each monomer is composed of two structurally distinct domains which are connected by a short polypeptide chain containing a cleavage-sensitive region (CSR).  The NTD is responsible for the DNA-binding character of the protein; in contrast, the CTD is integral in formation of the functional homodimer, cooperative-binding repression, and the auto-cleavage mechanism (Stayrook).  The principal purpose of the CSR is to provide a region which is both susceptible and insusceptible to cleavage depending upon the conformation the dimer assumes.  In addition, the CSR serves to stabilize interactions between chains in the dimer (2HNF).




==C-Terminal Domain (CTD)==
==C-Terminal Domain (CTD)==


The CTD of Lambda Repressor assumes a structural conformation similar to a knotted β-sheet and is composed of 104 amino acid resides (residues 132-236).  This conformation is key in establishing the dimer-forming interaction with the CTD of the opposite chain.  The CTD also facilitates the dimer-dimer interaction necessary for cooperative-binding repression. The active site of the auto-cleavage mechanism of Lambda Repressor is on the CTD.  Two amino acid residues mediate the auto-cleavage activity of the repressor, Lys192 and Ser149 (). <StructureSection load='3bdn' size='350' side='left' caption=' The auto-cleavage active site on the CTD is highlighted in yellow (residues 149, 192). (PDB entry [[3bdn]])' scene='Bacteriophage_Lambda_Repressor_cI/Ctd-_auto-cleavage_active_site/3'></StructureSection>
<StructureSection load='3bdn' size='350' side='left' caption='The octamer formed by interactions between CTDs of eight monomers.  Only the CTDs of the monomers are shown.  Polar (magenta) and nonpolar (grey) residues within the core of the protein are highlighted to show interactions between monomers.(PDB entry [[1KCA]])' scene='Bacteriophage_Lambda_Repressor_cI/Ctd-_auto-cleavage_active_site/3'>The CTD of Lambda Repressor assumes a structural conformation similar to a knotted β-sheet and is composed of 104 amino acid resides (residues 132-236).  This conformation is key in establishing the homodimer-forming interaction with the CTD of the opposite monomer.  The CTD also facilitates the dimer-dimer interaction necessary for cooperative-binding repression. Four homodimers complex together to form a functional <scene name='Bacteriophage_Lambda_Repressor_cI/Ctd_octamer/1'>octamer</scene> through cooperative-binding. This allows simultaneous repression of multiple non-adjacent promoter regions on the Lambda genome (1KCA). The active site of the auto-cleavage mechanism of Lambda Repressor is on the CTD.  Two amino acid residues mediate the auto-cleavage activity of the repressor, Lys192 and Ser149 (Stayrook).</StructureSection>
<StructureSection load='3bdn' size='350' side='left' caption='The CTD of Lambda Repressor chain A is highlighted in magenta (residues 132-236)(PDB entry [[3bdn]])' scene='Bacteriophage_Lambda_Repressor_cI/C-termianl_domain/1'></StructureSection>
<StructureSection load='3bdn' size='350' side='left' caption='The CTD of Lambda Repressor chain A is highlighted in magenta (residues 132-236)(PDB entry [[3bdn]])' scene='Bacteriophage_Lambda_Repressor_cI/C-termianl_domain/1'></StructureSection>


==Connecting Region==
==Connecting Region==
The region connecting the NTD to the CTD consists of 38 amino acid residues (residues 93-131) and contains the CSR.  The CSR is a long loop (residues 106-126) and serves to stabilize the dimer through interactions with the CSR of the opposite chain.  Cleavage occurs between Ala111 and Gly 112 in the CSR.  
 
<StructureSection load='3bdn' size='350' side='right' caption='The cleavage site of the connecting region is highlighted in red (residues 111-112), while the auto-cleavage active site of the CTD is highlighted in yellow(residues 149, 192). (PDB entry [[3bdn]])' scene='Bacteriophage_Lambda_Repressor_cI/Cleavage_site_and_active_site/1'></StructureSection>
<StructureSection load='3bdn' size='350' side='right' caption='The CSR, consisting of two residues (Ala 111 and Gly 112), is highlighted in red. Cleavage occurs at the peptide bond between these residues. (PDB entry [[2HNF]])' scene='Bacteriophage_Lambda_Repressor_cI/Csr/1'>The region connecting the NTD to the CTD consists of 38 amino acid residues (residues 93-131) and contains the CSR.  The CSR is on a long loop (residues 106-126) which serves to stabilize the homodimer through interactions with the connecting region of the opposite monomer.  Cleavage occurs between Ala 111 and Gly 112 in the CSR.</StructureSection>


==N-Terminal Domain (NTD)==
==N-Terminal Domain (NTD)==
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