Files 6PFK and 4PFK
  This is the crystal structure of a phosphofructokinase molecule that is bound to an inhibitor which mimics the action of PEP.  The enzyme is a tetramer.  To display only two of the subunits type the command ěrestrict *b or *cî
 Zoom in on the selected residues.  In the active R conformation the arg72 bridges the two substrates ATP and fructose-6-phosphate.  However in the inhibited T conformation (as seen here) the arg72 forms a salt bridge with glu241 and cannot interact with the substrates.  This is the only  change that the ATP binding site undergoes in switching from the R to T conformation.
 In contrast to the ATP binding site, the F6P binding site undergoes significant structural changes when the enzyme shifts from the R to T conformation.  Now zoom in on the selected residues.  Notice how in the T conformation the glu161 sticks directly into the binding pocket of fructose-6-phosphate.  Glu161ís negative charges causes the T conformation to have a very low binding affinity for F6P.  In the R conformation this glu will be replaced with an arg residue to facilitate binding of the substrate.  Also, observe the arg243, arg252, and glu222 residues.  It is thought that these residues also decrease substrate binding affinity in the T conformation by creating steric barriers which block the substrateís binding.  This magenta molecule is the inhibitor which mimics the action of PEP.  Notice how the inhibitor is not bound to the active site but rather to the allosteric binding site.  The binding of this inhibitor forces the enzyme to change itís conformation from the active R form to the inactive T form (seen here).  Notice how now, in the R conformation, the arg162 sticks toward the binding site (rather that the glu161).  Instead, the glu161 now forms a salt bridge with arg243.  This conformational change allows the arg162 to interact with the negatively charged phosphoryl group on the substrate and facilitates binding.
Primary Citation:

For 6PFK:  Schirmer, T., Evans, P. R.: Structural basis of the allosteric behaviour of phosphofructokinase.. Nature 343 pp. 140 (1990)

For 4PFK:  Evans, P. R., Farrants, G. W., Hudson, P. J.: Phosphofructokinase: structure and control..  Philos Trans R Soc Lond B Biol Sci 293 pp. 53 (1981)

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