## 8 Mechanism of the Rubisco Carboxylation Reaction: The Role of Broensted Acid-Base Catalysis
The new study [41] does not consider the RuBP enolization step but focuses on the subsequent elementary steps of the reaction coordinate (i.e., carboxylation, hydration, C2-C3 bond scission and C-2 protonation) shown in Figure 12.  
Results of the study [41] provide new insight into the following reaction steps which confirm the relevance of the acid-base chemistry: (i) the 2-carboxy-3-keto-arabinitol-1,5-diphosphate (3 in Figure 12) was shown to undergo protonation at the carboxylic group (affording the C2-carboxylic acid) to energetically facilitate the subsequent nucleophilic attack of OH\({}^{-}\) onto the C3 carbon leading the C3-gemodiolate 5; (ii) the C3-gemodiate was found to the most stable intermediate bound to the Mg\({}^{2+}\)-cation along the reaction coordinate, as shown from Relative Potential Energy calculations; (iii) the C2-C3 scission/C2-protonation events were described occurring in a concerted mechanism; (iv) Lys175-H\({}^{+}\) was established acting as proton source in step (iii). Figure 11: Structure of the FM21 model consisting of 339-342 atoms around the Mg\({}^{2+}\) cation. Where residues overlap visually, residues at the back are shown in gray and residues at the front are shown in thick black lines. Truncations from enzyme are highlighted as wavy lines in magenta. Only one water molecule coordinated to Mg\({}^{2+}\) is shown. (Figure 11 from ref. [41], used by permission of John Wiley and Sons (copyright © 2018)). It is worth noting that all the previously proposed reaction mechanisms have considered a two-step reaction consisting in the cleavage of the C2-C3 carbon bond, affording a C2-carbonin intermediate followed by stereospecific C2-carbon protonation to give 3-phospho-D-glycerate. Due to the novelty of the conclusion drawn in the previous work concerning the C2-C3 scission/C2-protonation steps occurring in a concerted mechanism, a more careful investigation was developed by [PERSON] et al., in 2019 [42] by applying ab initio molecular dynamic simulations on the molecular fragment FM21 (Figure 11 by using the Kohn-Sham density functional theory (Figure 13b). Figure 12: Mechanism for the steps following C2-carboxylate formation: (i) C2-carboxylic acid is formed by protonation from an unknown donor via solvent channels; (ii) C3-gemdiolate is formed as H2O approaches C3 and undergoes proton abstraction by KCX201; (iii) C2-C3 bond scission of the C3-gemdiolate, concerted with stereospecific C2-protonation by LYS175 and deprotonation of the C2-carboxylate acid by GLU60, yields product. (Figure 12 from ref. [41], adapted and used by permission of John Wiley and Sons (copyright © 2018)). Figure 13: (a) Mechanism of the C2-protonation steps occurring in a concerted mechanism, as proposed by [PERSON] et al., in 2019; (b) MEP (0 K) and PMF (298 K) plotted against the reaction coordinate (RC) defined as the difference between C2-C3 and C2-H distances. The C3-gemdiolate shown in Figure 12 is named “intermediate”. 3 PGA is named “products”. The legend shows the density functional used for energy calculation and the proton donor moiety for each reaction profile is indicated in parenthesis (either protonation directly from Lys175-H+ or via the Grothuss mechanism initiated by a phosphate proton and a single water molecule. Proton is highlighted in blue). (Figure 13 from ref. [42], adapted and used by permission of American Chemical Society (copyright © 2019)). By computing the variation of potential mean force (PMF at 298 K) and minimum potential energy (MPE at 0 K) along the reaction coordinate, the study intended to assess whether protonated Lys175-H+ or a proton translocation across a network of H-bonded water molecules with P1-group as proton donor (the so called phosphate mediated Grothus mechanism, Figure 13a) is involved in the stereospecific protonation of the C3-gemdiolate (\"intermediate\" in Figure 13b) to afford 3 PGA (\"products\" in Figure 13b).