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Title: Understanding the catalytic mechanism of xanthosine methyltransferase in caffeine biosynthesis from QM/MM molecular dynamics and free energy simulations

Journal Article · · Journal of Chemical Information and Modeling
 [1];  [2];  [3];  [4];  [5];  [3]
  1. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Shandong Agricultural Univ., Shandong (People's Republic of China)
  2. Univ. of Tennessee, Knoxville, TN (United States)
  3. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. Shandong Agricultural Univ., Shandong (People's Republic of China)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
+ Show Author Affiliations

S-Adenosyl-l-methionine (SAM) dependent xanthosine methyltransferase (XMT) is the key enzyme that catalyzes the first methyl transfer in the caffeine biosynthesis pathway to produce the intermediate 7-methylxanthosine (7mXR). Although XMT has been a subject of extensive discussions, the catalytic mechanism and nature of the substrate involved in the catalysis are still unclear. Here in this paper, quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy (potential of mean force or PMF) simulations are undertaken to determine the catalytic mechanism of the XMT-catalyzed reaction. Both xanthosine and its monoanionic form with N3 deprotonated are used as the substrates for the methylation. It is found that while the methyl group can be transferred to the monoanionic form of xanthosine with a reasonable free energy barrier (about 17 kcal/mol), that is not the case for the neutral xanthosine. The results suggest that the substrate for the first methylation step in the caffeine biosynthesis pathway is likely to be the monoanionic form of xanthosine rather than the neutral form as widely adopted. This conclusion is supported by the pKa value on N3 of xanthosine both measured in aqueous phase and calculated in the enzymatic environment. As a result, the structural and dynamics information from both the X-ray structure and MD simulations is also consistent with the monoanionic xanthosine scenario. Finally, we discuss the implications of this conclusion for caffeine biosynthesis.

Research Organization:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Science Foundation (NSF); National Nature Science Foundation of China
Grant/Contract Number:
AC05-00OR22725; ACI-1053575; 76335
OSTI ID:
1355886
Journal Information:
Journal of Chemical Information and Modeling, Vol. 56, Issue 9; ISSN 1549-9596
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 9 works
Citation information provided by
Web of Science

References (28)

Caffeine and related purine alkaloids: Biosynthesis, catabolism, function and genetic engineering journal February 2008
Caffeine biosynthesis and adenine metabolism in transgenic Coffea canephora plants with reduced expression of N-methyltransferase genes journal May 2006
The Structure of Two N -Methyltransferases from the Caffeine Biosynthetic Pathway journal April 2007
The coffee genome provides insight into the convergent evolution of caffeine biosynthesis journal September 2014
Quantum Mechanical/Molecular Mechanical Study of Catalytic Mechanism and Role of Key Residues in Methylation Reactions Catalyzed by Dimethylxanthine Methyltransferase in Caffeine Biosynthesis journal January 2014
The first committed step reaction of caffeine biosynthesis: 7-methylxanthosine synthase is closely homologous to caffeine synthases in coffee ( Coffea arabica L.) 1 journal June 2003
Essential Region for 3-N Methylation in N-Methyltransferases Involved in Caffeine Biosynthesis journal April 2010
Xanthine, xanthosine and its nucleotides: solution structures of neutral and ionic forms, and relevance to substrate properties in various enzyme systems and metabolic pathways. journal June 2004
CHARMM: The biomolecular simulation program journal July 2009
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations journal July 1983
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † journal April 1998
A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method journal January 2001
Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties journal September 1998
A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations journal July 1990
Comparison of simple potential functions for simulating liquid water journal July 1983
Active site dynamics in protein molecules: A stochastic boundary molecular-dynamics approach journal May 1985
Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison journal January 1988
THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method journal October 1992
Monte Carlo free energy estimates using non-Boltzmann sampling: Application to the sub-critical Lennard-Jones fluid journal October 1974
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values journal June 2011
A Preference for Edgewise Interactions between Aromatic Rings and Carboxylate Anions:  The Biological Relevance of Anion−Quadrupole Interactions journal July 2007
A Survey of Aspartate−Phenylalanine and Glutamate−Phenylalanine Interactions in the Protein Data Bank: Searching for Anion−π Pairs journal April 2011
QM/MM Free Energy Simulations of Salicylic Acid Methyltransferase: Effects of Stabilization of TS-like Structures on Substrate Specificity journal January 2011
Mechanism of histone methylation catalyzed by protein lysine methyltransferase SET7/9 and origin of product specificity journal May 2007
Catalytic Mechanism and Product Specificity of Rubisco Large Subunit Methyltransferase:  QM/MM and MD Investigations journal April 2007
How Do SET-Domain Protein Lysine Methyltransferases Achieve the Methylation State Specificity? Revisited by Ab Initio QM/MM Molecular Dynamics Simulations journal March 2008
Understanding Product Specificity of Protein Lysine Methyltransferases from QM/MM Molecular Dynamics and Free Energy Simulations: The Effects of Mutation on SET7/9 beyond the Tyr/Phe Switch journal January 2012
QM/MM MD and free energy simulations of the methylation reactions catalyzed by protein arginine methyltransferase PRMT3 journal July 2013

Cited By (3)

Efficient Computation of Free Energy Surfaces of Diels–Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level journal September 2018
Mechanism of the Dinuclear Iron Enzyme p ‐Aminobenzoate N‐oxygenase from Density Functional Calculations journal October 2018
Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase journal January 2018

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