Introduction
cI is a transcription inhibitor of bacteriophage Lambda. Also known as Lambda Repressor, cI is responsible for maintaining the lysogenic life cycle of phage Lambda. This is achieved when two repressor dimers bind cooperatively to adjacent operator sites on the DNA. The cooperative binding induces repression of the cro gene and simultaneous activation of the cI gene, which code for proteins Cro and cI, respectively (Stayrook et. al, 2008).
Structural Overview
The Lambda Repressor homodimer is composed of two identical polypeptide chains of 236 amino acid residues. The dimer is formed primarily 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 et. al, 2008). 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 (Ndjonka et. al, 2006). Four homodimers complex together to form a functional octamer through cooperative-binding. The octamer is formed by interactions between the CTDs of eight monomers. The CTDs of the octamer are shown to the right. Polar (magenta) and nonpolar (grey) residues within the core of the protein are highlighted to show some key interactions between monomers (PDB entry 1KCA). This allows simultaneous repression of promoter regions over 2.4 kb apart on the Lambda genome (Stayrook et. al, 2008).
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, PDB entry 1f39). 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. 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, Lys 192 and Ser 149 (Stayrook et. al, 2008).
Connecting Region
The region connecting the NTD to the CTD consists of 38 amino acid residues (residues 93-131) and contains the CSR (2hnf). 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. The natural structural conformation of the repressor is such that the auto-cleavage active site does not contact the CSR. During bacterial stress response, RecA binds to the repressor which induces a conformational change, bringing the CSR into contact with the auto-cleavage active site residues (Ndjonka et. al, 2006).
N-Terminal Domain (NTD)
<StructureSection load='3bdn' size='350' side='right' caption='The spacefill model of the NTD highlights the interactions between the repressor and DNA. (PDB entry 1lmb)' scene='Bacteriophage_Lambda_Repressor_cI/Ntd_spacefill/1'>The NTD Lambda repressor consists of the first 92 amino acid residues of the protein and contains the DNA-Binding Domain (Stayrook et. al, 2008) of the protein. The secondary structure of the NTD is a compact conformation of six alpha-helices. This secondary structure shows weak self-association, which is purported to aid in formation of the dimeric unit. The DNA-binding motif utilized by Lambda Repressor is a Helix-Turn-Helix (Beamer and Pabo, 1992). The Helix-Turn-Helix motifs of two dimerized NTDs are illustrated in red to the right.
