Sandbox Reserved 333: Difference between revisions

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==Structure==

:Mevalonate diphosphate decarboxylase exists as a symmetrical dimer<ref name = "Byres"/> <ref name = "Voynova"/> <ref name ="ByresMartin"/> . The C-terminal domains of each monomer are symmetrically oriented towards one another around a solvent-filled channel <ref name = "Byres"/>. The dimer is stabilized between alpha helices 6 and 10 on each monomer, and also through salt bridge interactions, tyrosine stacking, proline stacking, and hydrophobic interactions <ref name = "Byres"/>. The interface between the monomers is very small, with only 7% of the total surface area of the monomer engaged in the interface interaction <ref name = "Voynova"/>. This small interface between monomers is a characteristic of GHMP kinases <ref name = "Voynova"/>. Each monomer consists of a single polypeptide chain with 331 amino acid residues <ref name = "RCSB"> PMID: 6667333 </ref>. Each polypeptide chain has <scene name='Sandbox_Reserved_333/Alpha_helices/1'> 13 alpha helices </scene> and <scene name='Sandbox_Reserved_333/Beta_sheets/1'> 15 beta sheets </scene> <ref name ="RCSB"/>. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain <ref name = "Byres"/> . The active sites are located away from the solvent filled channel, and they are unaffected by dimerization <ref name = "Byres"/>. The amino acid residues Tyr19, Trp20, Trp158 and Met203 form a <scene name='Sandbox_Reserved_333/Hydrophobic_surfaces/1'>Hydrophobic surface</scene> that is important in the active site for helping to orient the Mevalonate diphosphate properly <ref name = "Byres"/>. One important animo acid in the active site is Tyrosine 19 (Fig 2) ~~<ref name = "Byres"/>. It~~ is strategically placed to interact with the terminal phosphate group of mevalonate diphosphate when it is bound in the active site <ref name = "Byres"/>. An ATP binding polypeptide segment called the P loop is also located near the active site <ref name = "Byres"/>. A total of 19 amino acid residue side chains are involved with substrate binding in the active site <ref name = "Byres"/>.

:Mevalonate diphosphate decarboxylase exists as a symmetrical dimer<ref name = "Byres"/> <ref name = "Voynova"/> <ref name ="ByresMartin"/> . The C-terminal domains of each monomer are symmetrically oriented towards one another around a solvent-filled channel <ref name = "Byres"/>. The dimer is stabilized between alpha helices 6 and 10 on each monomer, and also through salt bridge interactions, tyrosine stacking, proline stacking, and hydrophobic interactions <ref name = "Byres"/>. The interface between the monomers is very small, with only 7% of the total surface area of the monomer engaged in the interface interaction <ref name = "Voynova"/>. This small interface between monomers is a characteristic of GHMP kinases <ref name = "Voynova"/>. Each monomer consists of a single polypeptide chain with 331 amino acid residues <ref name = "RCSB"> PMID: 6667333 </ref>. Each polypeptide chain has <scene name='Sandbox_Reserved_333/Alpha_helices/1'> 13 alpha helices </scene> and <scene name='Sandbox_Reserved_333/Beta_sheets/1'> 15 beta sheets </scene> <ref name ="RCSB"/>. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain <ref name = "Byres"/> . The active sites are located away from the solvent filled channel, and they are unaffected by dimerization <ref name = "Byres"/>. The amino acid residues Tyr19, Trp20, Trp158 and Met203 form a <scene name='Sandbox_Reserved_333/Hydrophobic_surfaces/1'>Hydrophobic surface</scene> that is important in the active site for helping to orient the Mevalonate diphosphate properly <ref name = "Byres"/>. One important animo acid in the active site is Tyrosine 19 (Fig 2) because it is strategically placed to interact with the terminal phosphate group of mevalonate diphosphate when it is bound in the active site <ref name = "Byres"/>. An ATP binding polypeptide segment called the P loop is also located near the active site <ref name = "Byres"/>. A total of 19 amino acid residue side chains are involved with substrate binding in the active site <ref name = "Byres"/>.

[[Image:Tyrosine.png|thumb|left| Fig 2 Tyrosine 19 in the active site of mevalonate diphosphate decarboxylase.]]

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 ==Structure==
-:Mevalonate diphosphate decarboxylase exists as a symmetrical dimer<ref name = "Byres"/> <ref name = "Voynova"/> <ref name ="ByresMartin"/> . The C-terminal domains of each monomer are symmetrically oriented towards one another around a solvent-filled channel <ref name = "Byres"/>. The dimer is stabilized between alpha helices 6 and 10 on each monomer, and also through salt bridge interactions, tyrosine stacking, proline stacking, and hydrophobic interactions <ref name = "Byres"/>. The interface between the monomers is very small, with only 7% of the total surface area of the monomer engaged in the interface interaction <ref name = "Voynova"/>. This small interface between monomers is a characteristic of GHMP kinases <ref name = "Voynova"/>. Each monomer consists of a single polypeptide chain with 331 amino acid residues <ref name = "RCSB"> PMID: 6667333  </ref>. Each polypeptide chain has <scene name='Sandbox_Reserved_333/Alpha_helices/1'> 13 alpha helices </scene> and <scene name='Sandbox_Reserved_333/Beta_sheets/1'> 15 beta sheets </scene> <ref name ="RCSB"/>. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain <ref name = "Byres"/> . The active sites are located away from the solvent filled channel, and they are unaffected by dimerization <ref name = "Byres"/>. The amino acid residues Tyr19, Trp20, Trp158 and Met203 form a <scene name='Sandbox_Reserved_333/Hydrophobic_surfaces/1'>Hydrophobic surface</scene> that is important in the active site for helping to orient the Mevalonate diphosphate properly <ref name = "Byres"/>. One important animo acid in the active site is Tyrosine 19 (Fig 2) <ref name = "Byres"/>. It is strategically placed to interact with the terminal phosphate group of mevalonate diphosphate when it is bound in the active site <ref name = "Byres"/>. An ATP binding polypeptide segment called the P loop is also located near the active site <ref name = "Byres"/>.  A total of 19 amino acid residue side chains are involved with substrate binding in the active site <ref name = "Byres"/>.
+:Mevalonate diphosphate decarboxylase exists as a symmetrical dimer<ref name = "Byres"/> <ref name = "Voynova"/> <ref name ="ByresMartin"/> . The C-terminal domains of each monomer are symmetrically oriented towards one another around a solvent-filled channel <ref name = "Byres"/>. The dimer is stabilized between alpha helices 6 and 10 on each monomer, and also through salt bridge interactions, tyrosine stacking, proline stacking, and hydrophobic interactions <ref name = "Byres"/>. The interface between the monomers is very small, with only 7% of the total surface area of the monomer engaged in the interface interaction <ref name = "Voynova"/>. This small interface between monomers is a characteristic of GHMP kinases <ref name = "Voynova"/>. Each monomer consists of a single polypeptide chain with 331 amino acid residues <ref name = "RCSB"> PMID: 6667333  </ref>. Each polypeptide chain has <scene name='Sandbox_Reserved_333/Alpha_helices/1'> 13 alpha helices </scene> and <scene name='Sandbox_Reserved_333/Beta_sheets/1'> 15 beta sheets </scene> <ref name ="RCSB"/>. The active site on each monomer is a deep, highly charged cleft made up seven segments of polypeptide chain <ref name = "Byres"/> . The active sites are located away from the solvent filled channel, and they are unaffected by dimerization <ref name = "Byres"/>. The amino acid residues Tyr19, Trp20, Trp158 and Met203 form a <scene name='Sandbox_Reserved_333/Hydrophobic_surfaces/1'>Hydrophobic surface</scene> that is important in the active site for helping to orient the Mevalonate diphosphate properly <ref name = "Byres"/>. One important animo acid in the active site is Tyrosine 19 (Fig 2) because it is strategically placed to interact with the terminal phosphate group of mevalonate diphosphate when it is bound in the active site <ref name = "Byres"/>. An ATP binding polypeptide segment called the P loop is also located near the active site <ref name = "Byres"/>.  A total of 19 amino acid residue side chains are involved with substrate binding in the active site <ref name = "Byres"/>.
 [[Image:Tyrosine.png|thumb|left| Fig 2 Tyrosine 19 in the active site of mevalonate diphosphate decarboxylase.]]