Sandbox Reserved 774: Difference between revisions
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Has a four chain structure (<scene name='56/564050/Chain_a/1' target=0>A</scene>, <scene name='56/564050/Chain_b/1' target=0>B</scene>, <scene name='56/564050/Chain_c/1' target=0>C</scene>, <scene name='56/564050/Chain_d/1' target=0>D</scene>) with 2.4 A resolution, and 2.9 A resolution with a co-factor (acetyl-CoA). Core fold features include four conserved sequence motifs of the GNAT family and comprises a central highly curved five stranded <scene name='56/564050/Beta_sheets/1' target=0>β-sheets</scene> surrounded on both sides by helical segments.<ref name=Shiva/> | Has a four chain structure (<scene name='56/564050/Chain_a/1' target=0>A</scene>, <scene name='56/564050/Chain_b/1' target=0>B</scene>, <scene name='56/564050/Chain_c/1' target=0>C</scene>, <scene name='56/564050/Chain_d/1' target=0>D</scene>) with 2.4 A resolution, and 2.9 A resolution with a co-factor (acetyl-CoA). Core fold features include four conserved sequence motifs of the GNAT family and comprises a central highly curved five stranded <scene name='56/564050/Beta_sheets/1' target=0>β-sheets</scene> surrounded on both sides by helical segments.<ref name=Shiva/> | ||
Each monomer has a similar and compact α-β structure. The structure's core contains a central mixed five-stranded sheet structure from sheets β1 to β5. Strands β1 to β4, however, are organized in an anti-parallel arrangement while β4 and β5 are parallel, but only at their amino-terminal ends. At the other end of the parallel β4 and β5 strands, they are spread apart because of a β bulge in strand β4 caused by residue N74 of strand β3 as well as N91 and D92 of β4. The central sheet is accompanied on each side by two α-helices. Helices α1 and α2 are on one side of the sheet with α1 lying nearly flat against and perpendicular to other direction of the strands, while helices α3 and α4 are on the opposite side of the sheet with helix α3 cupped within the curved face of the sheet. <ref name=Shiva/> The method used to determine the structure was [[X-ray crystallography]]. Sedimentation and crystal structure analysis clearly shows that Hpa2 is dimeric in solution and tetramerizes in the unit crystal. The crystal structure of the oligomer reveals that two Hpa2 dimers are held together by interaction between the bound acetyl-CoA molecules. The average B-factor value | Each monomer has a similar and compact α-β structure. The structure's core contains a central mixed five-stranded sheet structure from sheets β1 to β5. Strands β1 to β4, however, are organized in an anti-parallel arrangement while β4 and β5 are parallel, but only at their amino-terminal ends. At the other end of the parallel β4 and β5 strands, they are spread apart because of a β bulge in strand β4 caused by residue N74 of strand β3 as well as N91 and D92 of β4. The central sheet is accompanied on each side by two α-helices. Helices α1 and α2 are on one side of the sheet with α1 lying nearly flat against and perpendicular to other direction of the strands, while helices α3 and α4 are on the opposite side of the sheet with helix α3 cupped within the curved face of the sheet. <ref name=Shiva/> The method used to determine the structure was [[X-ray crystallography]]. Sedimentation and crystal structure analysis clearly shows that Hpa2 is dimeric in solution and tetramerizes in the unit crystal. The crystal structure of the oligomer reveals that two Hpa2 dimers are held together by interaction between the bound acetyl-CoA molecules. The average B-factor value of the <scene name='56/564050/Bakhbone_mainechain/1' target=0>main chain</scene> is 23.9 with a 25.4 <scene name='56/564050/Sidechain/2' target=0>side chain</scene>. The R-factor is 0.19. <ref name=Shiva/> | ||
[[Image:Chain.jpg.png | thumb | '''Figure 1.''' Sequence of Hpa2.]] | [[Image:Chain.jpg.png | thumb | '''Figure 1.''' Sequence of Hpa2.]] | ||
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The binding of substrates and release of products can be random, fully ordered, or a combination of both. It operates on a Bi-Bi mechanism. A study that employed product inhibitors CoA and acetylated (Lys14Ac) H3 peptide and dead-end inhibitor desulfo-CoA in order to determine the order of substrate binding has yielded results consistent with a fully ordered Bi-Bi kinetic mechanism where AcCoA is the first substrate to bind, and CoA is the last product that is released. It is also important to note that the transcriptional co-activator GCN5 from yeast (yGCN5) is a histone acetyltransferase that is essential for the activation of target genes. Bi-substrate kinetic analysis using acetyl-coenzyme A and an H3 histone synthetic peptide indicated that both substrates must bind to form a ternary complex before catalysis. Product inhibition studies revealed that the product CoA was a competitive inhibitor as opposed to AcCoA. Desulfo-CoA, a dead end inhibitor, also demonstrated simple competitive inhibition versus AcCoA. Acetylated (Lys14Ac) H3 peptide displayed noncompetitive inhibition against both H3 peptide and AcCoA.<ref>Tanner, et al. "Kinetic Mechanism of the Histone Acetyltransferase GCN5 from Yeast." J. Biol. Chem. 275.29 (2000): 2-9. Web. 26 Nov. 2013.</ref> | The binding of substrates and release of products can be random, fully ordered, or a combination of both. It operates on a Bi-Bi mechanism. A study that employed product inhibitors CoA and acetylated (Lys14Ac) H3 peptide and dead-end inhibitor desulfo-CoA in order to determine the order of substrate binding has yielded results consistent with a fully ordered Bi-Bi kinetic mechanism where AcCoA is the first substrate to bind, and CoA is the last product that is released. It is also important to note that the transcriptional co-activator GCN5 from yeast (yGCN5) is a histone acetyltransferase that is essential for the activation of target genes. Bi-substrate kinetic analysis using acetyl-coenzyme A and an H3 histone synthetic peptide indicated that both substrates must bind to form a ternary complex before catalysis. Product inhibition studies revealed that the product CoA was a competitive inhibitor as opposed to AcCoA. Desulfo-CoA, a dead end inhibitor, also demonstrated simple competitive inhibition versus AcCoA. Acetylated (Lys14Ac) H3 peptide displayed noncompetitive inhibition against both H3 peptide and AcCoA.<ref>Tanner, et al. "Kinetic Mechanism of the Histone Acetyltransferase GCN5 from Yeast." J. Biol. Chem. 275.29 (2000): 2-9. Web. 26 Nov. 2013.</ref> | ||
[[Image:Hpa2_Kinetic_Mechanism.jpg]][[Image:Kinetic_Mechanism.jpg]] | [[Image:Hpa2_Kinetic_Mechanism.jpg]] [[Image:Kinetic_Mechanism.jpg]] | ||
==Chemical Mechanism== | ==Chemical Mechanism== | ||