A Tale of Two Acids: When Arginine Is a More Appropriate Acid than H3O+

• Type: Article in International Scientific Journal
• Date: 2010

Authors

Pedro J Silva (Author) Other; Claudia Schulz (Author) Other; Dieter Jahn (Author) Other; Martina Jahn (Author) Other; Maria Joao Ramos (Author) FCUP

Journal

Title: Journal of Physical Chemistry B

Vol. 114

Pages: 8994-9001

ISSN: 1520-6106

Publisher: American Chemical Society

Indexing

ISI Web of Knowledge - 11 Citations

Scopus - 10 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-003-4VA

DOI: 10.1021/jp100961s

Abstract (EN): Uroporphyrinogen 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 of uroporphyrinogen III decarboxylase is substrate protonation rather than the decarboxylation reaction. This protonation can be effected by an arginine residue (Arg37) in close proximity to the substrate. In this report, we present evidence for the function of this arginine residue as a general acid catalyst. Although substrate protonation by H3O+ is both exergonic and very fast, our density functional calculations show that 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. Consequently, H3O+ can be excluded from a role in both protonations proposed for the enzyme mechanism. In agreement with these conclusions, a second arginine residue (Arg41) is uniquely positioned to act as donor of the second proton, with an activation barrier below 2 kcal mol(-1). Generated mutant uroporphyrinogen III decarboxylase variants carrying amino acid exchanges in the position of both arginine residues (R41A, R41K, R37A, and R37K) failed to produce coproporphyrinogen III. The proposed unusual use of two basic residues as general acids in two different proton donation steps by uroporphyrinogen III decarboxylase provides 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 8