Sandbox Reserved 957: Difference between revisions
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* A N-terminal cyclin-fold region with eight helixes [26]: 5 α-helixes (1, 3, 5, 6 and 8) and 3 310-helixes (2,4, and 7),<scene name='60/604476/537_678/3'> from the 537th to the 678th residues</scene>.<br \> | * A N-terminal cyclin-fold region with eight helixes [26]: 5 α-helixes (1, 3, 5, 6 and 8) and 3 310-helixes (2,4, and 7),<scene name='60/604476/537_678/3'> from the 537th to the 678th residues</scene>.<br \> | ||
* A linker domain: two antiparallels α9 and α10 helixes, and between a disordered region,<scene name='60/604476/679-725/2'>from the 679th to the 725th residues</scene>.<br \> | * A linker domain: two antiparallels α9 and α10 helixes, and between a disordered region,<scene name='60/604476/679-725/2'>from the 679th to the 725th residues</scene>.<br \> | ||
* A C-terminal buddle pocket with eight helixes: 5 long α-helixes (11, 12, 14, 17 and 18) and 3 smaller helixes (13, 15 and 16),<scene name='60/604476/726-860/ | * A C-terminal buddle pocket with eight helixes: 5 long α-helixes (11, 12, 14, 17 and 18) and 3 smaller helixes (13, 15 and 16),<scene name='60/604476/726-860/2'> from the 726th to the 860th residues</scene>.<br \> | ||
** α5, 6 and 8 surround α3 and form an interface with the linker domain and the CTD.<br \> | ** α5, 6 and 8 surround α3 and form an interface with the linker domain and the CTD.<br \> | ||
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M site contains:<br \> | M site contains:<br \> | ||
* The Me-1 and Me-2 sites are occupied by metal ions, Zinc within Me-1 and within Me-2, Zinc, Magnesium or Manganese [5],<br \> | * The Me-1 and Me-2 sites are occupied by metal ions, Zinc within Me-1 and within Me-2, Zinc, Magnesium or Manganese [5],<br \> | ||
* The residues His617, Asp654, Asp764, His653 and two H2O (W1 et W2) binding zinc:<br \> | * The residues <scene name='60/604476/His617_asp654_asp764_his653/1'>His617, Asp654, Asp764, His653</scene> and two H2O (W1 et W2) binding zinc:<br \> | ||
** The crucial Asp764 [3] and the conserved His617 and 653[4], which bind one Zinc ion, are fundamental for the catalytic activity.<br \> | ** The crucial <scene name='60/604476/Asp764/1'>Asp764</scene> [3] and the conserved His617 and 653[4], which bind one Zinc ion, are fundamental for the catalytic activity.<br \> | ||
** Zinc is critical for catalytic activity, but it isn't implied in the formation of the hydrophobic pocket. In fact, even if the His617and 653 are lost and so the Zn not bound, a massive addition of Manganese[4] in the medium allows a reactivation of catalysis.<br \> | ** <scene name='60/604476/Zn/1'>Zinc</scene> is critical for catalytic activity, but it isn't implied in the formation of the hydrophobic pocket. In fact, even if <scene name='60/604476/His653_his617/1'>the His617and 653</scene> are lost and so the Zn not bound, a massive addition of Manganese[4] in the medium allows a reactivation of catalysis.<br \> | ||
* W2 binds Zn and Mg [24],<br \> | * W2 binds | ||
<scene name='60/604476/Mg_zn/1'>Zn and Mg</scene> [24],<br \> | |||
* And there are 3 hydrogen bonds between 3 H2O and the conserved resides His657, Asp682 and His685 [24].<br \> | * And there are 3 hydrogen bonds between 3 H2O and the conserved resides His657, Asp682 and His685 [24].<br \> | ||
Q site contains:<br \> | Q site contains:<br \> | ||
* In particular the conserved residues | * In particular the conserved residues Gln817, Phe820, Val782 and Tyr612. [24]<br \> | ||
* The hydrogen bonds, between | * The hydrogen bonds, between Gln817 and 775, Gln775 and Ala767, Gln775 and Trp853, imply an interaction between Gln817 and the cGMP purine. Thus, it improves the specificity for the cGMP, against cAMP. [24]<br \> | ||
* And | * And Tyr612, Val782, Leu785 an Phe820 bind the cGMP through this pyrazol ring and π-π interactions between Gln817 and the phenyl ring. [24]<br \> | ||
** So, the conserved hydrophobic residue | ** So, the conserved hydrophobic residue Tyr 612 is critical in the maintaining of the affinity. [3]<br \> | ||
H site:<br \> | H site:<br \> | ||