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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
Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.
Örebro University, School of Science and Technology. (Biofysisk kemi)
Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, N9B 3P4, Canada.
Örebro University, School of Science and Technology.
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2011 (English)In: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 32, no 5, p. 822-834Article in journal (Refereed) Published
Abstract [en]

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 protontransfer 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 activesite residues as well as several other functional groups.

Place, publisher, year, edition, pages
New York: John Wiley & Sons, 2011. Vol. 32, no 5, p. 822-834
Keyword [en]
uroporphyrinogen decarboxylase III, uroporphyrinogen III, porphyrin biosynthesis, quantum mechanics/molecular mechanics and density functional theory
National Category
Natural Sciences Physical Chemistry Physical Chemistry Theoretical Chemistry Theoretical Chemistry
Research subject
Biochemistry
Identifiers
URN: urn:nbn:se:oru:diva-13964DOI: 10.1002/jcc.21661ISI: 000288400600007PubMedID: 20941734Scopus ID: 2-s2.0-79951968121OAI: oai:DiVA.org:oru-13964DiVA: diva2:387692
Note

Leif A. Eriksson is also affiliated to School of Chemistry, National University of Ireland, Galway, Ireland

Available from: 2011-01-14 Created: 2011-01-14 Last updated: 2017-12-11Bibliographically approved

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Erdtman, EdvinEriksson, Leif A.

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