## 7 Conformational Changes during Catalysis: \"Open\" and \"Closed\" Form of the Enzyme  
In an interesting study [PERSON] et al. (2008) have compared X-ray crystal structures of Rubisco from spinach, tobacco and _Synecococcus_ considering either \"empty active site\" proteins (i.e., polypeptides bearing the ECM complex but lacking substrate binding) and sugar phosphate-bound forms of Rubisco (including RuBP, 2 CABP or XuBP ligands). Careful comparison of structures allowed identification of a complex sequence of conformational changes occurring during transition from the so called \"open\" (with the active site accessible to solvent) to \"closed\" states of the protein. Occurrence of catalysis requires the enzyme to lie in the \"closed\" state with the active site not accessible to the solvent. After enzyme activation (i.e., ECM-complex formation as described in Section 4) Rubisco remains in an \"open\" conformation schematically depicted in Figure 8a. Figure 8a (open state) shows a view from the central axis of the TIM barrel of the L1-subunit (referred  
Figure 7: Structure of the active site of activated 2 CABP-bound Rubisco plotted from the 8 RUC.PDB file (Protein Data Bank) showing the coordination environment of Mg\({}^{2+}\) as proposed by [PERSON] et al., in 2008. Residues with an asterisk in the label are from N-terminal domain of the antiparallel L subunit. Numbering of amino acid residues is based on that of spinach Rubisco (Figure from ref. ([PERSON] et al., 2008), adapted and used by permission of American Chemical Society (copyright © 2008). as \"active site exposed\") which is partially \"covered\" by the N-terminal domain of the juxtaposed L2 subunit. In the \"open state\", Figure 8a shows loop 6 is in a retracted position, and shows the C-terminal helical domain (composed of amino acid residues from Trp462 to the C-terminus) pointing far from the active site. Once RuBP binds tightly to the active site, the enzyme transits from the \"open\" to the \"closed\" conformation shown in Figure 8a. The catalytic site is schematized evidencing location of the Mg\({}^{2+}\) as well as the P1- and P2-binding sites of the sugar phosphates. Figure 8: (**a**) Schematic illustration of the “open” to “closed” state transition of the catalytic site of Rubisco. The “open” to “closed” transition occurs through a sequence of three main conformational changes; (**b**) evidences the binding sites for 1P- and 5P-groups of RuBP (in red) in Rubisco from the cyanobacterium _Synechocystis_ sp. The third phosphate group shown (in the latch-site) is assigned a particular role in the regulation of catalysis (Figure 8a from ref. [38], used by permission of Elsevier (copyright 2000); Figure 8b from ref. [39], adapted and used by permission of American Society of Microbiology (copyright © 2005)). The \"open\" to \"closed\" transition occurs through a sequence of three main conformational changes: (i) first the N-terminal domain of the L subunit rotates as a semi-rigid body occluding the entrance of the TIM barrel (i.e., the sugar phosphates binding pocket); (ii) loop 6 extends in a position that occludes the active site; (iii) the C-terminal strand overlaps with loop 6. It is worth noting that \"open\" state conformation is also observed in X-ray crystal structures of proteins bearing 2 CABP bound to the inactivated (metal-free) active site or RuBP bound to the catalytically inert Ca\({}^{2+}\). In the latter cases, sugar phosphates bind the active site quite weakly. Taking a closer look at the tertiary structure conformational changes occurring during open-to-closed transition, [PERSON] et al., propose that a central role is played by binding of the two phosphate anions of ribulose-1,5-bisphosphate to specific active site positions.