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Sandbox108

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==Glutamine synthetase assignment by UMBC undergraduate students==
==Glutamine synthetase assignment by UMBC undergraduate students==
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{{STRUCTURE_2qc8 | PDB=2qc8 | SCENE= }}
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{{STRUCTURE_2gls | PDB=2gls | SCENE= }}
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<scene name='User:Taewang_Lee/Exercise_2/1'>Exercise 2</scene>
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<scene name='User:Taewang_Lee/Exercise_3/5'>Exercise 3</scene>
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<scene name='Sandbox108/Exercise_4/1'>Exercise 4</scene>
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<scene name='User:Taewang_Lee/Exercise_4/5'>Exercise 4(Practiced)</scene>
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== OUTLINE ==
 
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''Tertiary Structure''
 
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''Glutamine synthetase of Salmonella typhimurium''
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Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] and has two domains in refined atomic model of glutamine synthetase from Salmonella typhimurium. Hydrophobic interaction is a major driving force determining the most tertiary structure of the proteins. [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] Hydrogen bonding <insert wiki showing the H.B> is crucial in stabilizing the tertiary structure as well. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds <insert wiki showing the disulfide bonds of cysteine> between cysteine residues stabilize the tertiary structure. [http://webhost.bridgew.edu/fgorga/proteins/proteins.htm]
 
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Glutamine synthetase from Salmonella has twenty three helix-helix interactions and is four different types of interactions. [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2gls&template=protein.html&o=HELIX_INTERACTIONS&l=1&s=1&c=7&chain=A] Hydrophobic/polar <hydrophobic/polar wiki> (put color) and hydrophilic <hydrophilic wiki>(put color) region of glutamine are combined together to fold proteins.
 
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Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain [http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html] and mostly affected by <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene>(<scene name='Sandbox108/Polar/1'>polar(blue)</scene>) interaction and hydrogen bonding. In general, hydrophobic interaction is a major driving force determining the most tertiary structure of the proteins. Hydrogen bonding is crucial in stabilizing the tertiary structure as well.[http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] Also, disulfide bonds stabilize the tertiary structure in residues such as cysteine residues.[http://webhost.bridgew.edu/fgorga/proteins/proteins.htm] However, for Salmonella typhimurium it is mostly influenced by the helix-helix interactions between 12-subunits enzymes within two layers.[http://www.stanford.edu/group/pandegroup/folding/education/prstruc.html]
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is within uncharged polar <insert wiki showing the uncharged polar groups>. Usually, uncharged polar groups are classified as hydrophilic <insert wiki showing the hydrophilic> that is found on the outside of proteins. Also, amino acids with the character of acidic or basic side chains are polar, showing on the outside of molecules <insert wiki showing the polar>. For glutamine, its side chain is uncharged and formed by replacing the hydroxyl of glutamic acid with an amine functional group. [http://en.wikipedia.org/wiki/Glutamine] In the other hand, glutamine has no side chain on non-polar group, however the side chain on non-polar groups of the proteins usually tends to be hydrophobic <insert wiki showing the hydrophobic of cysteine> and to cluster together on the inside.[http://www.bmb.uga.edu/wampler/tutorial/prot3.html]
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Glutamine synthetase from Salmonella typhimurium is the 12-subunits enzyme, and has 23 helix-helix interactions involving helices of chain A with four different types of interactions. [http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=2gls&template=protein.html&o=HELIX_INTERACTIONS&l=1&s=1&c=7&chain=A] The 12-subunits enzyme are arranged in two layers of six, such as <scene name='Sandbox108/Glu_131/1'>Glu-131</scene> which is the one of the protein residues of Salmonella typhimurium; at the interface of pairs of subunits within each layer, six anti-parallel beta strands formed cylindrical active sites.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Each active site holds two <scene name='Sandbox108/Mn/3'>Mn2+</scene> ions surrounded by some <scene name='Sandbox108/Histidyl_side_chain/1'>histidyl side chains.</scene> [http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Also, the protein ligands to Mn2+ 469 are <scene name='Sandbox108/Glu_131/3'>Glu-131</scene>, <scene name='Sandbox108/Glu_212/3'>Glu-212</scene>, and <scene name='Sandbox108/Glu_220/2'>Glu-220</scene>; those to Mn2+ 470 are <scene name='Sandbox108/Glu_129/2'>Glu-129</scene>, <scene name='Sandbox108/His_269/1'>His-269</scene>, and <scene name='Sandbox108/Glu_357/2'>Glu-357</scene>.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Glutamine from Salmonella typhimurium has 12-subunits of each of them in pairs within two layers. C-terminus end of the polypetide and a helical thong, which inserts into a <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> pocket formed by two neighboring subunits on the opposite ring, hold the two layers of subunits tightly.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] Also, <scene name='Sandbox108/Hydrogen_bonded_beta-sheet/1'>hydrogen-bonded beta sheet interactions(black)</scene> can affect the form of tertiary structure, but <scene name='Sandbox108/Hydrophobic/1'>Hydrophobic(purple)</scene> interactions will contribute to the stability of the intersubunit between two layers more efficiently.[http://www.ncbi.nlm.nih.gov/pubmed/2572586?dopt=Abstract] In the other hand, the most effective interaction in glutamine synthetase from Salmonella typhimurium is the helix-helix interactions. The folding of the proteins can be affected by the 12-subunits in the residues. In the case of Salmonella typhimurium the helices of chain A has <scene name='Sandbox108/Charged_region/1'>the charged regions(blue and red)</scene>, while most glutamine has uncharged side chain which formed by replacing the hydroxyl of glutamic acid with an amine functional group. Moreover, glutamine from Salmonella typhimurium has two domains; "beta-grasp domain" and "catalytic domain."[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam03951][http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00120] In short, this is N-terminal and C-terminal domain.[http://www.rcsb.org/pdb/explore/explore.do?structureId=2GLS] The N-terminal domain refers to the end of a polypeptide which has a free amine group,[http://en.wikipedia.org/wiki/N-terminal_domain] and the C-terminal end of the polypeptide has a free carboxyl group.[http://en.wikipedia.org/wiki/C-terminus] As a result, glutamine synthetase for Salmonella typhimurium depends mostly on the helix-helix interactions involving helices with four different types of interactions. 12-subunits enzymes are arranged in two layers of six, where the hydrogen-bonded beta sheet and hydrophobic interactions occur.

Current revision

Glutamine synthetase assignment by UMBC undergraduate students

PDB ID 2gls

Drag the structure with the mouse to rotate
2gls, resolution 3.50Å ()
Ligands:
Activity: Glutamate--ammonia ligase, with EC number 6.3.1.2
Resources: FirstGlance, OCA, PDBsum, RCSB
Coordinates: save as pdb, mmCIF, xml




Glutamine synthetase of Salmonella typhimurium


Tertiary structure of protein is characterized by the “global” folding of a polypeptide chain [1] and mostly affected by () interaction and hydrogen bonding. In general, hydrophobic interaction is a major driving force determining the most tertiary structure of the proteins. Hydrogen bonding is crucial in stabilizing the tertiary structure as well.[2] Also, disulfide bonds stabilize the tertiary structure in residues such as cysteine residues.[3] However, for Salmonella typhimurium it is mostly influenced by the helix-helix interactions between 12-subunits enzymes within two layers.[4]


Glutamine synthetase from Salmonella typhimurium is the 12-subunits enzyme, and has 23 helix-helix interactions involving helices of chain A with four different types of interactions. [5] The 12-subunits enzyme are arranged in two layers of six, such as which is the one of the protein residues of Salmonella typhimurium; at the interface of pairs of subunits within each layer, six anti-parallel beta strands formed cylindrical active sites.[6] Each active site holds two ions surrounded by some [7] Also, the protein ligands to Mn2+ 469 are , , and ; those to Mn2+ 470 are , , and .[8] Glutamine from Salmonella typhimurium has 12-subunits of each of them in pairs within two layers. C-terminus end of the polypetide and a helical thong, which inserts into a pocket formed by two neighboring subunits on the opposite ring, hold the two layers of subunits tightly.[9] Also, can affect the form of tertiary structure, but interactions will contribute to the stability of the intersubunit between two layers more efficiently.[10] In the other hand, the most effective interaction in glutamine synthetase from Salmonella typhimurium is the helix-helix interactions. The folding of the proteins can be affected by the 12-subunits in the residues. In the case of Salmonella typhimurium the helices of chain A has , while most glutamine has uncharged side chain which formed by replacing the hydroxyl of glutamic acid with an amine functional group. Moreover, glutamine from Salmonella typhimurium has two domains; "beta-grasp domain" and "catalytic domain."[11][12] In short, this is N-terminal and C-terminal domain.[13] The N-terminal domain refers to the end of a polypeptide which has a free amine group,[14] and the C-terminal end of the polypeptide has a free carboxyl group.[15] As a result, glutamine synthetase for Salmonella typhimurium depends mostly on the helix-helix interactions involving helices with four different types of interactions. 12-subunits enzymes are arranged in two layers of six, where the hydrogen-bonded beta sheet and hydrophobic interactions occur.

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