The structure of porphobilinogen deaminase has been determined by X-ray crystallography with approximate dimensions of 57 x 43 x 32(in angstroms)(5,8). The structure is composed of three domains of about equal size with the catalytic cleft located between domains 1(blue) and 2(yellow). Each of the domains are mixed alpha/beta structures. Domain 1 and domain 2 are both comprised of a parallel beta sheet, made up of four parallel strands and one anti-parallel strand, with alpha helices packed on either side. A duplication of the alpha-beta-alpha motif in the parallel beta sheet allows the hydrophobic core of both domains to be made from the tight packing of hydrophobic side chains from the beta strands and adjacent alpha helices. Domain 3 is an open faced anti-parallel beta sheet covered on one side by three alpha helices. The hydrophobic core of this domain is largely made up from small aliphatic side chains projecting from the two longer, roughly parallel alpha helices(5). The dipyrromethane cofactor is covalently linked to cysteine-242, located on a loop from domain 3, and projects into the catalytic cleft between domains 1 and 2. The apoenzyme self-assembles the cofactor using two molecules of porphobilinogen. Binding of the first porphobilinogen unit(C1) to the active site region results in deamination to the azafulvene and subsequent reaction with the deprotonated cysteinyl sulfhydryl group. The second porphobilinogen unit(C2) is also deaminated to the azafulvene species but the nucleophilic attack instead comes from the free alpha position of the C1 pyrrole. Carbon-carbon bond formation between the two pyrrole units completes the cofactor assembly process. Cofactor assembly and stabilization is made possible by numerous polar interactions with the active site of the enzyme. In addition, substantial conformational changes occur as a result of cofactor binding, protecting it from catalytic turnover and making the holoenzyme much more heat labile than the apoenzyme(2,3,4,5,7,8).