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

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 p K a value on N3 of xanthosine both measured in aqueous phase and calculated in the enzymatic environment. As a result, the structural and dynamicsmore » 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.« less
Authors:
 [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)
Publication Date:
Grant/Contract Number:
AC05-00OR22725; ACI-1053575; 76335
Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Information and Modeling
Additional Journal Information:
Journal Volume: 56; Journal Issue: 9; Journal ID: ISSN 1549-9596
Publisher:
American Chemical Society
Research Org:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org:
USDOE Office of Science (SC); National Science Foundation (NSF); National Nature Science Foundation of China
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1355886