Sandbox Reserved 1072: Difference between revisions

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==Catalytic GGEEF Domain==

The <scene name='69/694239/Ggeef_domain_zmout_dgcz/2'>GGEEF domain</scene> of DgcZ is part of the GGDEF family of proteins that includes a conserved sequence, GG[DE][DE]F[3].The GGEEF domain is a homodimer consisting of a central five-stranded β-sheet surrounded by five α-helices. The GGEEF domain contains two catalytic half sites that, when combined together in a productive conformation, form the entire <scene name='69/694239/Ggeef_domain_dgcz/6'>active site</scene>. Residues Gly-206, Gly-207, Glu-208, Glu-209, and Phe-210 form the active site. Each <scene name='69/694239/Ggeef_domain_half_site_dgcz/4'>half-site</scene> binds one GTP molecule. DgcZ binds the guanine base of GTP through hydrogen bonds to <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. 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[1].

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/2'>Magnesium ion</scene> (Mg2+) stabilizes the negative charges on the phosphate groups. 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.

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> (Mg2+) stabilizes the negative charges on the phosphate groups. 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.

===Mechanism of Action===

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 ==Catalytic GGEEF Domain==
 The <scene name='69/694239/Ggeef_domain_zmout_dgcz/2'>GGEEF domain</scene> of DgcZ is part of the GGDEF family of proteins that includes a conserved sequence, GG[DE][DE]F<sup>[3]</sup>.The GGEEF domain is a homodimer consisting of a central five-stranded β-sheet surrounded by five α-helices. The GGEEF domain contains two catalytic half sites that, when combined together in a productive conformation, form the entire <scene name='69/694239/Ggeef_domain_dgcz/6'>active site</scene>. Residues Gly-206, Gly-207, Glu-208, Glu-209, and Phe-210 form the active site.  Each <scene name='69/694239/Ggeef_domain_half_site_dgcz/4'>half-site</scene> binds one GTP molecule. DgcZ binds the guanine base of GTP through hydrogen bonds to <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. 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>[1]</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/2'>Magnesium ion</scene> (Mg<sup>2+</sup>) stabilizes the negative charges on the phosphate groups. 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.
+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 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.
 ===Mechanism of Action===