Sandbox Reserved 1072: Difference between revisions
From Proteopedia
Jump to navigationJump to search
David Emch (talk | contribs) No edit summary |
David Emch (talk | contribs) No edit summary |
||
| Line 14: | Line 14: | ||
==Catalytic GGEEF Domains== | ==Catalytic GGEEF Domains== | ||
The <scene name='69/694239/Ggeef_domain_zmout_dgcz/3'>GGEEF domains</scene> of DgcZ are part of the GGDEF family of proteins that are characterized by a conserved sequence, GG[DE][DE]F<sup>[6]</sup>. The GGEEF domains contain a central five-stranded β-sheet surrounded by five α-helices (Figure 4). The GGEEF domains each possess a catalytic half-site (residues Gly-206, Gly-207, Glu-208, Glu-209, and Phe-210) that, when combined together in a productive conformation, form the entire <scene name='69/694239/Ggeef_domain_dgcz/6'>active site</scene>. Each | The <scene name='69/694239/Ggeef_domain_zmout_dgcz/3'>GGEEF domains</scene> of DgcZ are part of the GGDEF family of proteins that are characterized by a conserved sequence, GG[DE][DE]F<sup>[6]</sup>. The GGEEF domains contain a central five-stranded β-sheet surrounded by five α-helices (Figure 4). The GGEEF domains each possess a <scene name='69/694239/Ggeef_domain_half_site_dgcz/5'>catalytic half-site</scene> (residues Gly-206, Gly-207, Glu-208, Glu-209, and Phe-210) that, when combined together in a productive conformation, form the entire <scene name='69/694239/Ggeef_domain_dgcz/6'>active site</scene>. Each half-site binds the guanine base of a single GTP molecule via hydrogen bonding to residues <scene name='69/694239/Gtp_guanine_bonds_asn_asp_dgcz/7'>Asn 173 and Asp 182</scene>. This scene depicts an inactive form of the protein because it was crystallized with zinc bound, destroying the active conformation of GGEEF domains. The ribose of each guanosine triphosphate, and subsequent product c-di-GMP riboses, are held only loosely by the enzyme, while the phosphate groups are not bound to the active site at all<sup>[3]</sup>. | ||
The alpha phosphate is available for attack by the 3 prime hydroxyl group on another GTP. A <scene name='69/694239/Gtp_magnesium_cofactors_dgcz/3'>Magnesium ion</scene> (Mg<sup>+2</sup>) stabilizes the negative charges on the phosphate groups. When in the inactive conformation, the C3 of the ribose on one GTP is <scene name='69/694239/Gtp_distances/2'>too far away</scene> (9-10 Angstroms) from the alpha phosphate on the other GTP to undergo cyclization. When in the productive conformation, each GTP is held in close proximity with the α-phosphate groups overlapping C3 of the ribose ring. This conformation allows the α-phospate of one GTP to react with the alcohol group attached to C3 of the ribose on the second GTP, resulting in a cyclization of the two molecules into c-di-GMP<sup>[3]</sup>. | The alpha phosphate is available for attack by the 3 prime hydroxyl group on another GTP. A <scene name='69/694239/Gtp_magnesium_cofactors_dgcz/3'>Magnesium ion</scene> (Mg<sup>+2</sup>) stabilizes the negative charges on the phosphate groups. When in the inactive conformation, the C3 of the ribose on one GTP is <scene name='69/694239/Gtp_distances/2'>too far away</scene> (9-10 Angstroms) from the alpha phosphate on the other GTP to undergo cyclization. When in the productive conformation, each GTP is held in close proximity with the α-phosphate groups overlapping C3 of the ribose ring. This conformation allows the α-phospate of one GTP to react with the alcohol group attached to C3 of the ribose on the second GTP, resulting in a cyclization of the two molecules into c-di-GMP<sup>[3]</sup>. | ||
