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Tian BX, Erdtman E, Eriksson LA. Catalytic mechanism of porphobilinogen synthase: the chemical step revisited by QM/MM calculations. J Phys Chem B 2012; 116:12105-12. [PMID: 22974111 DOI: 10.1021/jp304743c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
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.
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Affiliation(s)
- Bo-Xue Tian
- School of Chemistry, National University of Ireland-Galway, Galway, Ireland
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Erdtman E, Bushnell EAC, Gauld JW, Eriksson LA. Computational Insights into the Mechanism of Porphobilinogen Synthase. J Phys Chem B 2010; 114:16860-70. [DOI: 10.1021/jp103590d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Edvin Erdtman
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
| | - Eric A. C. Bushnell
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
| | - James W. Gauld
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
| | - Leif A. Eriksson
- School of Science and Technology, Örebro Life Science Center and Modeling and Simulation Research Center, Örebro University, Örebro, Sweden; Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada; and School of Chemistry, NUI Galway, Galway, Ireland
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