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An Enzymatic Atavist Revealed in Dual Pathways for Water Activation

By Donghong Min, Helen R Josephine, Hongzhi Li, Clemens Lakner, Iain S MacPherson, Gavin J. P Naylor, David Swofford, Lizbeth Hedstrom and Wei Yang

Abstract

Inosine monophosphate dehydrogenase (IMPDH) catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinct catalytic residues. How did Nature construct such a complicated catalyst? Here we employ a “Wang-Landau” metadynamics algorithm in hybrid quantum mechanical/molecular mechanical (QM/MM) simulations to investigate the mechanism of the hydrolase reaction. These simulations show that the lowest energy pathway utilizes Arg418 as the base that activates water, in remarkable agreement with previous experiments. Surprisingly, the simulations also reveal a second pathway for water activation involving a proton relay from Thr321 to Glu431. The energy barrier for the Thr321 pathway is similar to the barrier observed experimentally when Arg418 is removed by mutation. The Thr321 pathway dominates at low pH when Arg418 is protonated, which predicts that the substitution of Glu431 with Gln will shift the pH-rate profile to the right. This prediction is confirmed in subsequent experiments. Phylogenetic analysis suggests that the Thr321 pathway was present in the ancestral enzyme, but was lost when the eukaryotic lineage diverged. We propose that the primordial IMPDH utilized the Thr321 pathway exclusively, and that this mechanism became obsolete when the more sophisticated catalytic machinery of the Arg418 pathway was installed. Thus, our simulations provide an unanticipated window into the evolution of a complex enzyme

Topics: Research Article
Publisher: Public Library of Science
OAI identifier: oai:pubmedcentral.nih.gov:2525682
Provided by: PubMed Central

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Citations

  1. (2002). A branch-andbound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: application to the evolution of five gene families.
  2. (1990). A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations.
  3. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximumlikelihood approach.
  4. (1986). Ab initio and Monte Carlo calculations for a nucleophilic addition reaction in the gas phase and in aqueous solution.
  5. (1998). All-atom empirical potential for molecular modeling and dynamics studies of proteins.
  6. (1990). Basic local alignment search tool.
  7. (2000). Catalytic activity of the D38A mutant of 3-oxoDelta 5-steroid isomerase: recruitment of aspartate-99 as the base.
  8. (1983). CHARMM: a program for macromolecular energy, minimization, and dynamics calculations.
  9. (2002). Chemical rescue in catalysis by human carbonic anhydrases II and III.
  10. (1999). Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems.
  11. (2006). Crystal structure of human guanosine monophosphate reductase 2 (GMPR2) in complex with GMP.
  12. (1988). Dissecting the catalytic triad of a serine protease.
  13. (1995). Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search.
  14. (2001). Enzyme catalysis: removing chemically ‘essential’ residues by site-directed mutagenesis.
  15. (2002). Escaping free-energy minima.
  16. (2005). Evolution of enzymatic activities in the orotidine 59-monophosphate decarboxylase suprafamily: structural basis for catalytic promiscuity in wild-type and designed mutants of 3-keto-L-gulonate 6-phosphate decarboxylase.
  17. (2003). Evolution of function in (beta/alpha)8-barrel enzymes.
  18. (2006). Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee.
  19. (2001). Generalized solvent boundary potential for computer simulations.
  20. (1997). Genetic contributions to understanding polyketide synthases.
  21. (2005). Guanidine derivatives rescue the Arg418Ala mutation of Tritrichomonas foetus IMP dehydrogenase.
  22. (1990). Histidine-40 of ribonuclease T1 acts as base catalyst when the true catalytic base, glutamic acid-58, is replaced by alanine.
  23. (2000). Homology among (betaalpha)(8) barrels: implications for the evolution of metabolic pathways.
  24. (1996). Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry.
  25. (1999). IMP dehydrogenase: mechanism of action and inhibition.
  26. (2006). IMP dehydrogenase: structural schizophrenia and an unusual base.
  27. (2005). Is Arg418 the catalytic base required for the hydrolysis step of the IMP dehydrogenase reaction?
  28. (1999). Kinetic mechanism of Tritrichomonas foetus inosine-59-monophosphate dehydrogenase.
  29. (1993). Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites.
  30. (2006). Metadynamics as a tool for exploring free energy landscapes of chemical reactions.
  31. (1970). Microbial modification of mycophenolic acid.
  32. (2003). MrBayes 3: Bayesian phylogenetic inference under mixed models.
  33. (2001). Multimodular biocatalysts for natural product assembly.
  34. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput.
  35. (2002). NADPH-dependent GMP reductase isoenzyme of human (GMPR2). Expression, purification, and kinetic properties.
  36. (2006). Natural biocombinatorics in the polyketide synthase genes of the actinobacterium Streptomyces avermitilis.
  37. (1988). Nucleotide sequence of the gene encoding the GMP reductase of Escherichia coli K12.
  38. (2007). Ohno’s dilemma: evolution PLoS Biology | www.plosbiology.org
  39. (2007). On the convergence improvement in the metadynamics simulations: a Wang-Landau recursion approach.
  40. (2002). One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions.
  41. (2004). Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference.
  42. (2003). PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sunderland (Massachusetts): Sinauer Associates.
  43. (1979). Reaction mechanism and specificity of human GMP reductase.
  44. (1969). Recombination in Escherichia coli. 3. Mapping by the gradient of transmission.
  45. (2005). Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules.
  46. (1998). Selfconsistent-charge density-functional tight-binding method for simulations of complex materials properties.
  47. (1999). Species-specific inhibition of inosine 59-monophosphate dehydrogenase by mycophenolic acid.
  48. (2004). Substitution of the conserved Arg-Tyr dyad selectively disrupts the hydrolysis phase of the IMP dehydrogenase reaction.
  49. (2000). T-Coffee: a novel method for fast and accurate multiple sequence alignment.
  50. (2005). The functional basis of mycophenolic acid resistance in Candida albicans IMP dehydrogenase.
  51. (2003). The immunosuppressive agent mizoribine monophosphate forms a transition state analog complex with IMP dehydrogenase.
  52. (1976). Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme.
  53. (2004). UCSF Chimera—a visualization system for exploratory research and analysis.

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