Author ORCID Identifier
https://orcid.org/0000-0002-2956-9781
Document Type
Article
Publication Date
10-2011
Publication Title
Journal of Computational Chemistry
Volume
32
Issue
5
First Page
822
Last Page
834
Abstract
In humans, uroporphyrinogen decarboxylase is intimately involved in the synthesis of heme, where the decarboxylation of the uroporphyrinogen‐III occurs in a single catalytic site. Several variants of the mechanistic proposal exist; however, the exact mechanism is still debated. Thus, using an ONIOM quantum mechanical/molecular mechanical approach, the mechanism by which uroporphyrinogen decarboxylase decarboxylates ring D of uroporphyrinogen‐III has been investigated. From the study performed, it was found that both Arg37 and Arg50 are essential in the decarboxylation of ring D, where experimentally both have been shown to be critical to the catalytic behavior of the enzyme. Overall, the reaction was found to have a barrier of 10.3 kcal mol−1at 298.15 K. The rate‐limiting step was found to be the initial proton transfer from Arg37 to the substrate before the decarboxylation. In addition, it has been found that several key interactions exist between the substrate carboxylate groups and backbone amides of various active site residues as well as several other functional groups.
DOI
10.1002/jcc.21661
Recommended Citation
Bushnell, Eric Andre; Erdtman, Edvin; Llano, Jorge; Eriksson, Leif A.; and Gauld, James. (2011). The first branching point in porphyrin biosynthesis: A systematic docking, molecular dynamics and quantum mechanical/molecular mechanical study of substrate binding and mechanism of uroporphyrinogen‐III decarboxylase. Journal of Computational Chemistry, 32 (5), 822-834.
https://scholar.uwindsor.ca/chemistrybiochemistrypub/133