Structure of the Active Site:

There are 15 helices and 7 beta sheets making up the secondary structure of AGAT.  Of the helices, 8 are alpha helices, and the other 7 are 310 helices.  Of all 15 helices, only one actually contributes anything (Arg 169) to the active site other than helping deliver the substrates and products to where they need to go.  In addition, the beta sheets seem to contribute nothing to the active site, or to the narrow tunnel with which the substrate is delivered to the active site.  All other active components of the active site are in what is known as a "random coil" conformation.

The active site consists of several amino acid residues, all being contributed by a pseudosymmetrical series of five beta-beta-alpha-beta subunits.   These form the narrow channel to the active site, which has basket-like handles to help guide and hold the substrate in place.  There are five beta-beta-alpha-beta subunits forming the central active site.  These subunits can be seen by clicking here:  

The key active site residues are His 303, Cys 407, and Asp 254.   It is known that the nucleophilic cysteine is deprotonated by the histidine in order to remove the guanidyl end of the arginine side chain.  It is not known, however, precisely what the aspartic acid residue is for, but a 2000 fold decrease in activity is caused simply by a mutation into aspartamine.  It is believed that the aspartic acid residue removes the proton from histidine.  The active site with ornithine can be best seen here:  

Overall, the cysteine is deprotonated, attacks the aminidyl group of arginine to form ornithine.  Ornithine leaves the active site and is replaced by glycine.  The amino terminus of glycine then receives the aminidyl group from the cysteinyl residue and is subsequently  deprotonated by His 303 to form a stable glycocyamine guanidoacetate molecule.

Other contributing residues seem to include His 303 , which destabilizes the amidino bonds and donates hydrogens, Asp 254 , which seems to deprotonate the histidine, and then Arg169 and His 406 , which seems to occupy the carboxyl terminus of glycine in order to withdraw electrons from the molecule and direct the reaction to the amino terminus of glycine.   Unfortunately, no images of glycine bound into the active site were available upon publication, but this seems quite likely considering the active site.

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