User:Youngsen Jeng: Difference between revisions

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==Project==
==Project==


{{STRUCTURE_2qc8 |  PDB=2qc8 |  SCENE=  }}
{{STRUCTURE_2gls |  PDB=2gls |  SCENE=  }}




== Glutamine Synthetase Exercise 1 by Youngsen&Youngdae ==
'''Outline of the Project'''
Exercise 1<scene name='Rainbow/Rainbow10/1'>Glutamine synthetase with N-terminal blue C-terminal red</scene>Dr Gluick's class


== Glutamine Synthetase Exercise 2 by Youngsen&Youngdae ==
Glutamine synthetase(GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of <scene name='User:Youngsen_Jeng/12_identical_subunits/1'>12 identical subunits</scene> The activity of Glutamine Synthetase I-type enzyme is controlled by the <scene name='User:Youngsen_Jeng/Adenylation_of_a_tyrosine/2'>adenylation of tyrosine residue</scene><br>
Exercise 2<scene name='Rainbow/Labeled_ligand_in_chain_a/3'>Labeled Ligands in Chain A</scene>Dr. Gluick's class


The positively charged monovalent cation contributes to the structural stability of GS. Ginsburg and Stadtman(1973) concluded that dodecameric E. coli Glutamine Synthetase is stabilized by <scene name='User:Youngsen_Jeng/Mn2/2'>Mn2+</scene>, and that monovalent cations stabilize of the quaternary structure of GS. Stabilization by the monovalent cation may be due both to the electrostatic effects of its positive charge and to other components of the energy of the metal-protein bonding. Interactions of the positively charged monovalent cation with the negatively charged substrate glutamate, <scene name='User:Youngsen_Jeng/Glu_212/1'>Glu 212</scene>, <scene name='User:Youngsen_Jeng/Ser_53/1'>Ser 53</scene>, and <scene name='User:Youngsen_Jeng/Asp_50/1'>Asp 50</scene> could strengthen the active conformation<'''Insert wiki here'''>. Because Ser 53’and Asp 50’reside at the subunit contact surface, the monovalent cation enhances the “side to side” intersubunit interaction.


== Glutamine Synthetase Exercise 3 by Youngsen&Youngdae ==
Structural stabilization of Glutamine Synthetase by divalent cations, especially by the n1 ion<'''Insert wiki here'''>, has been ascribed to the attraction of their positive charges to the negative charges of glutamate and ATP and of their ligands<'''Insert wiki here'''> (Liaw et al., 1993~).
Exercise 3<scene name='Rainbow/Active_site_residues/1'>Active Site Amino Acid Residues with ligands</scene>Dr Gluick's class


== Glutamine Synthetase Exercise 4 by Youngsen&Youngdae ==
The structure of the dodecamer exposes several beta loops which are important in stabilizing quaternary structure of Glutamine Synthetase. One beta loop consists of <scene name='User:Youngsen_Jeng/Beta_loop_156-173/1'>hydrophilic residues</scene> 156-173, projects into the <scene name='User:Youngsen_Jeng/Beta_loop_projecting/1'>central channel</scene> of the dodecamer. Another beta loop is the <scene name='User:Youngsen_Jeng/Beta_loop_with_tyr_397/1'>adenylation loop</scene>, so called because it contains tyrosyine residue 397 which is covalently modified by addition of AMP.


Exercise 4<scene name='User:Youngsen_Jeng/Residue_f63_g319/1'>Salt bridge between F63 and G319</scene>Dr Gluick's class


'''FINAL PROJECT'''


== Outline of the project(revised) ==
Glutamine synthetase(GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. Glutamine Synthetase I is prokaryotic enzyme and it is consisted of oligomers of <scene name='User:Youngsen_Jeng/12_identical_subunits/1'>12 identical subunits</scene>. The activity of Glutamine Synthetase I-type enzyme is controlled by the <scene name='User:Youngsen_Jeng/Adenylation_of_a_tyrosine/2'>adenylation of tyrosine residue</scene><br>.<ref>Gill, H & Eisenberg, D., Biochemistry 2001 40: 1903-1912</ref>


Glutamine synthetase(GS) is an enzyme that plays an essential role in the metabolism of nitrogen by catalyzing the condensation of glutamate and ammonia to form glutamine. Class I enzymes (GSI) are specific to prokaryotes, and are oligomers of <scene name='User:Youngsen_Jeng/12_identical_subunits/1'>12 identical subunits</scene> The activity of Glutamine Synthetase I-type enzyme is controlled by the <scene name='User:Youngsen_Jeng/Adenylation_of_a_tyrosine/2'>adenylation of tyrosine residue</scene><br>  
The positively charged monovalent cation contributes to the structural stability of GS. Ginsburg and Stadtman(1973) concluded that dodecameric E. coli Glutamine Synthetase is stabilized by <scene name='User:Youngsen_Jeng/Mn2/2'>Mn2+</scene>, and that monovalent cations stabilize of the quaternary structure of Glutamine Synthetase. Stabilization by the monovalent cation may be due both to the electrostatic effects of its positive charge and to other components of the energy of the metal-protein bonding. Interactions of the positively charged monovalent cation with the negatively charged substrate glutamate, <scene name='User:Youngsen_Jeng/Glu_212/1'>Glu 212</scene>, <scene name='User:Youngsen_Jeng/Ser_53/1'>Ser 53</scene>, and <scene name='User:Youngsen_Jeng/Asp_50/1'>Asp 50</scene> could strengthen the active conformation. Because Ser 53’and Asp 50’reside at the subunit contact surface, the monovalent cation enhances the “side to side” intersubunit interaction.<ref>Liaw, S-H, et.al.,Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site Protein Sci. 1995 4: 2358-2365</ref>


The positively charged monovalent cation contributes to the structural stability of GS. Ginsburg and Stadtman(1973) concluded that dodecameric E. coli Glutamine Synthetase is stabilized by <scene name='User:Youngsen_Jeng/Mn2/2'>Mn2+</scene>, and that monovalent cations stabilize of the quaternary structure of GS. Stabilization by the monovalent cation may be due both to the electrostatic effects of its positive charge and to other components of the energy of the metal-protein bonding. Interactions of the positively charged monovalent cation with the negatively charged substrate glutamate, <scene name='User:Youngsen_Jeng/Glu_212/1'>Glu 212</scene>, <scene name='User:Youngsen_Jeng/Ser_53/1'>Ser 53</scene>, and Asp 50’ could strengthen the active conformation<'''Insert wiki here'''>. Because Ser 53’and Asp 50’reside at the subunit contact surface, the monovalent cation enhances the “side to side” intersubunit interaction.
The structure of the dodecamer exposes several beta loops which are important in stabilizing quaternary structure of Glutamine Synthetase. One beta loop consists of <scene name='User:Youngsen_Jeng/Beta_loop_156-173/1'>hydrophilic residues</scene> 156-173, projects into the <scene name='User:Youngsen_Jeng/Beta_loop_projecting/1'>central channel</scene> of the dodecamer. Another beta loop is the <scene name='User:Youngsen_Jeng/Beta_loop_with_tyr_397/1'>adenylation loop</scene>, so called because it contains tyrosyine residue 397 which is covalently modified by addition of AMP.<ref>Eisenberg, D., et.al., Structure-function relationships of glutamine synthetases, Biochim Biophys Acta 2000: 1477, 122-145</ref>


Structural stabilization of Glutamine Synthetase by divalent cations, especially by the n1 ion<'''Insert wiki here'''>, has been ascribed to the attraction of their positive charges to the negative charges of glutamate and ATP and of their ligands<'''Insert wiki here'''> (Liaw et al., 1993~).
=References=
<references/>
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