Opening Image: The head-tail connector of bacteriophage phi29 is composed of 12 identical subunits. It is the central component of a rotary motor that packages the viral genomic DNA into the preformed capsid shell of the virus. Hydrolysis of ATP powers the motor and drives the dsDNA into the prohead. trace model.
PKCI: Protein Kinase C Inhibitor
Surface model of protein kinase C inhibitor.
Isolate the interface of chain A. The hydrophobic residues that form the contact surface are shown in white. Note the presence of a lone water molecule lying on the hydrophobic contact surface.
cartoon model of chain A. Describe the tertiary structure in one or two sentences. Does the tertiary structure provide any insights into the interactions holding the two subunits together?
PKCI: Hydrogen Bonding Partners
We've isolated one chain of PKCI. exposed hydrogen-bonding groups (3 peptide carbonyl oxygen atoms and 3 peptide amide nitrogen groups) lie along the outermost edge of β-sheet. What are six hydrogen-bonding sites doing in an otherwise completely hydrophobic region?
surface model with hydrophobicity colored from high to low.
Remember that the two subunits of PKCI are identical. Consequently, the contact surfaces are not only identical, they are complementary to each other. So what happens to the exposed hydrogen-bonding groups when one subunit is rotated to bring the two complementary surfaces come together to form the dimer?
PKCI: Interchain β-sheet
As you can see, the outer edge of the β-sheet of one subunit is precisely complementary to the outer edge of the other β-sheet and six new hydrogen bonds are buried in the hyrophobic core.
Association of the two subunits is guided by hydrogen bonding between the complementary edges of the two β-sheets. The result is a continuous interchain β-sheet. This is your first -- but not the last -- encounter with the important concept of using the exposed edges of β-sheets to form continuous interchain β-sheets as a key protein-protein interaction motif.
Finally, this transparent model gives you one last look at the lone water molecule at the center of the hydrophobic core. Note that the entire molecule rotates about this water molecule. "Why?" is a question we will answer later in this chapter.
The Met repressor is complexed with co-repressor and DNA. The functional protein is a homotetramer composed of two homodimers. The co-repressor, S-adenosylmethionine, is displayed as a spacefilling model; binding sites for the co-repressor lie in a crevice between the homodimers.
S-Adenosylmethionine (SAM) is a key cofactor for the biological transfer of methyl groups. It is synthesized from ATP and methionine by the action of methionine adenosyl transferase. SAM is a potent methylating agent by virtue of the sulfonium ion (Me–S+–R2). The activated methyl group is subject to attack by nucleophiles. One example is the methylation of DNA in methyl-directed mismatch repair. View for the structural formula of SAM.
The Subunit Interface in the A·B Homodimer
Surface model of the dimer.
Cartoon model of the dimer.
Isolate the dimer interface of chain B. The hydrophobic residues of chain B that make contact with chain A are shown in white. Two SAM molecules are also included in the representation of the dimer interface.
Display chain A as a cartoon. Note that chain A has a single β-strand which actually passes through a loop formed by chain B.
Zoom in on the interchain hydrogen bonds between the two single β-strands.