Silva, Pedro J.Schulz, ClaudiaJahn, DieterJahn, MartinaRamos, Maria João2012-08-022012-08-022010Silva, Pedro J., Schulz, Claudia, Jahn, Dieter, Jahn, Martina, Ramos, Maria João (2010). A Tale of Two Acids: When Arginine Is a More Appropriate Acid than H3O+. The Journal of Physical Chemistry B, 114 (27), 8994-9001. DOI: 10.1021/jp100961s. ISSN 1520-6106.1520-6106http://hdl.handle.net/10284/3291Uroporphyrinogen III decarboxylase catalyzes the fifth step in heme biosynthesis: the elimination of carboxyl groups from the four acetate side chains of uroporphyrinogen-III to yield coproporphyrinogen-III. We have previously found that the rate-limiting step is substrate protonation, rather than decarboxylation itself, and that this protonation can be effected by a nearby arginine residue (Arg37). In this report, we have studied the reasons for the unusual choice of arginine as a general acid catalyst. Our density functional calculations show that, although substrate protonation by H3O+ is both exergonic and very fast, in the presence of a protonated Arg37 substrate decarboxylation becomes rate-limiting and the substrate spontaneously breaks upon protonation. These results suggest that the active site must be shielded from solvent protons, and that therefore H3O+ should be excluded from a role in both protonations present in this mechanism. A second Arg residue (Arg41) is uniquely positioned to act as donor of the second proton, with an activation barrier below 2 kcal mol-1. Additional site-directed mutagenesis experiments confirmed that no coproporphyrinogen is formed in the absence of any of these these Arg residues. This counter-intuitive use of two basic residues as general acids in two different proton donation steps by uroporphyrinogen decarboxylase may have arisen as an elegant solution to the problem of simultaneously binding the very negative uroporphyrinogen (which requires a positively charged active site), and selectively protonating it while preventing excessive carboxylate stabilization by positive charges.engUroporphyrinogen decarboxylaseReaction mechanismDecarboxylationDensity-functional theoryBinding/unbinding eventsjournal article