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
| Autor: | James W. Gauld, Jorge Llano, Leif A. Eriksson, Edvin Erdtman, Eric A. C. Bushnell |
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| Rok vydání: | 2010 |
| Předmět: |
Models
Molecular Porphyrins Decarboxylation Stereochemistry Uroporphyrinogen III decarboxylase Molecular Conformation macromolecular substances Molecular Dynamics Simulation chemistry.chemical_compound Theoretical chemistry Humans Uroporphyrinogen Decarboxylase Heme Quantum Biochemistry Biophysics and Structural Biology Binding Sites Porphyrin biosynthesis Computational Biology Substrate (chemistry) General Chemistry Chemistry Computational Mathematics chemistry Uroporphyrinogen III Biocatalysis Quantum Theory |
| Zdroj: | Chemistry and Biochemistry Publications |
| ISSN: | 0192-8651 |
| DOI: | 10.1002/jcc.21661 |
| Popis: | 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(-1) at 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. |
| Databáze: | OpenAIRE |
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