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Catalytic Mechanism of Porphobilinogen Synthase: The Chemical Step Revisited by QM/MM Calculations
Högskolan i Borås, Institutionen Ingenjörshögskolan.
2012 (engelsk)Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 116, nr 40, s. 12105-12112Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Porphobilinogen synthase (PBGS) catalyzes the asymmetric condensation and cyclization of two 5-aminolevulinic acid (5-ALA) substrate molecules to give porphobilinogen (PBG). The chemical step of PBGS is herein revisited using QM/MM (ONIOM) calculations. Two different protonation states and several different mechanisms are considered. Previous mechanisms based on DFT-only calculations are shown unlikely to occur. According to these new calculations, the deprotonation step rather than ring closure is rate-limiting. Both the C–C bond formation first mechanism and the C–N bond formation first mechanism are possible, depending on how the A-site ALA binds to the enzyme. We furthermore propose that future work should focus on the substrate binding step rather than the enzymatic mechanism.

sted, utgiver, år, opplag, sider
American Chemical Society , 2012. Vol. 116, nr 40, s. 12105-12112
Emneord [en]
Enzymes, QM/MM, Simulation, Reaction mechanism, Porphobilinogen synthase, Resursåtervinning
HSV kategori
Identifikatorer
URN: urn:nbn:se:hb:diva-1418DOI: 10.1021/jp304743cISI: 000309648900005PubMedID: 22974111Lokal ID: 2320/11733OAI: oai:DiVA.org:hb-1418DiVA, id: diva2:869473
Tilgjengelig fra: 2015-11-13 Laget: 2015-11-13 Sist oppdatert: 2017-10-17bibliografisk kontrollert

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