Karen Bulaklak/Sandbox1 Glucosamine 6 Phosphate Synthase
From Proteopedia
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== Discussion == | == Discussion == | ||
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A 3-dimensional model of Glucosamine-6-phosphate synthase was created highlighting vital features of the protein’s isomerase domain: | A 3-dimensional model of Glucosamine-6-phosphate synthase was created highlighting vital features of the protein’s isomerase domain: | ||
| - | *The UDP-GlcNAc binding pocket | + | *The <scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/Udp_binding_pocket/2'>UDP-GlcNAc binding pocket</scene> includes the sidechains Gly474, Val476, Ser484, Thr487, His492 and residues 489-491. |
| - | **Coordinates with metal cation | + | **Coordinates with <scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/Udp_na_ion/1'>metal cation</scene> when <scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/Udp_liganded/1'>substrate</scene> is bound, possibly indicating that a positive charge is needed to increase the stability of the enzyme-substrate complex. |
| - | *Fructose-6-phosphate | + | *<scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/F6p/1'>Fructose-6-phosphate</scene> interacts with <scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/F6p_binding_site/3'>sidechains</scene> of Glu591, Lys588, His607. These residues form a small binding domain for F6P, which has yet to be completely characterized. |
*These two important binding sites appear on opposite sides of each chain, perhaps indicating that the substrates do not greatly effect each others’ interaction with the protein. | *These two important binding sites appear on opposite sides of each chain, perhaps indicating that the substrates do not greatly effect each others’ interaction with the protein. | ||
| - | *Tetramerization sites create a horizontal line of symmetry across the protein, separating identical subunits (A and D, B and C), a so-called “dimer of dimers.” | + | *<scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/Tetramerization_sites/1'>Tetramerization sites</scene> create a horizontal line of symmetry across the protein, separating identical subunits (A and D, B and C), a so-called “dimer of dimers.” |
| - | *Beta sheets | + | *<scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/Beta_sheets/1'>Beta sheets</scene> could also provide internal support to the protein. |
A physical model of the isomerase domain, the main ligand binding structure of the protein, can aid in the understanding of its multiple substrate interactions and necessary conformations for enzymatic activity. | A physical model of the isomerase domain, the main ligand binding structure of the protein, can aid in the understanding of its multiple substrate interactions and necessary conformations for enzymatic activity. | ||
Future projects may include creating physical models of possible drug that target binding domains or other areas of glucosamine-6-phosphate, highlighting catalytic sites and modeling the prokaryotic form of the protein to compare their activity. With this new tool, we can propose ways to inhibit substrate binding, and consequently, the metabolic pathway of C. Albicans. | Future projects may include creating physical models of possible drug that target binding domains or other areas of glucosamine-6-phosphate, highlighting catalytic sites and modeling the prokaryotic form of the protein to compare their activity. With this new tool, we can propose ways to inhibit substrate binding, and consequently, the metabolic pathway of C. Albicans. | ||
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| - | <scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/Serine/1'>Serine</scene> <scene name='Karen_Bulaklak/Sandbox1_Glucosamine_6_Phosphate_Synthase/Secondary_structures/1'>Secondary structures</scene> | ||
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| - | <applet load='2put' size='300' frame='true' align='right' caption='Insert caption here' /> | ||
Revision as of 04:34, 8 December 2009
Discussion
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A 3-dimensional model of Glucosamine-6-phosphate synthase was created highlighting vital features of the protein’s isomerase domain:
- The includes the sidechains Gly474, Val476, Ser484, Thr487, His492 and residues 489-491.
- Coordinates with when is bound, possibly indicating that a positive charge is needed to increase the stability of the enzyme-substrate complex.
- interacts with of Glu591, Lys588, His607. These residues form a small binding domain for F6P, which has yet to be completely characterized.
- These two important binding sites appear on opposite sides of each chain, perhaps indicating that the substrates do not greatly effect each others’ interaction with the protein.
- create a horizontal line of symmetry across the protein, separating identical subunits (A and D, B and C), a so-called “dimer of dimers.”
- could also provide internal support to the protein.
A physical model of the isomerase domain, the main ligand binding structure of the protein, can aid in the understanding of its multiple substrate interactions and necessary conformations for enzymatic activity.
Future projects may include creating physical models of possible drug that target binding domains or other areas of glucosamine-6-phosphate, highlighting catalytic sites and modeling the prokaryotic form of the protein to compare their activity. With this new tool, we can propose ways to inhibit substrate binding, and consequently, the metabolic pathway of C. Albicans.
