Proteopedia - User contributions [en]

Sandbox 1551

2019-04-22T23:03:26Z

Tom Gluick: the nest

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='2qc8' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox 1551'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==
practice scene <scene name='77/777614/Serration/1'>I see red</scene>

== Structural highlights ==

The labels of the synthetase with ligands too; <scene name='77/777614/The_ligands_of_the_synthetase/1'>Text To Be Displayed</scene>
This is an example with a echo or label at the end showing all the ligands with some zooming. <scene name='77/777614/Ligand_with_echo/1'>Ligand with Echo</scene>

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox 1551

2019-04-22T03:50:10Z

Tom Gluick:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='2qc8' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox 1551'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

The labels of the synthetase with ligands too; <scene name='77/777614/The_ligands_of_the_synthetase/1'>Text To Be Displayed</scene>
This is an example with a echo or label at the end showing all the ligands with some zooming. <scene name='77/777614/Ligand_with_echo/1'>Ligand with Echo</scene>

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox 1551

2019-04-21T04:25:14Z

Tom Gluick:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='4v7i' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Sandbox 1551'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

The labels of the synthetase with ligands too; <scene name='77/777614/The_ligands_of_the_synthetase/1'>Text To Be Displayed</scene>

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1544

2019-02-12T00:39:43Z

Tom Gluick:

{{ Sandbox_Reserved_GGC_BHCM4100_1}}
==Structure==
<StructureSection load='1ege' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

tttttt

== Function ==
3. poppy

== Disease ==
there is no dies
== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1544

2019-02-12T00:38:10Z

Tom Gluick: /* Structure */

{{ Sandbox_Reserved_GGC_BHCM4100_1}}
==Structure==
<StructureSection load='1ege' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

tttttt

== Function ==
3. poppy

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

Sandbox Reserved 1544

2019-02-12T00:36:01Z

Tom Gluick: /* Function */

{{ Sandbox_Reserved_GGC_BHCM4100_1}}
==Structure==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==
3. poppy

== Disease ==

== Relevance ==

== Structural highlights ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

User:Tom Gluick

2019-02-10T22:24:02Z

Tom Gluick:

<nowiki><nowiki>Insert non-formatted text here</nowiki></nowiki>I earned a Ph.D. in Chemistry in 1980 from the Chemistry Department of the University of Montana. After a lengthy prodoctoral stint at Johns Hopkins Unviersity, I was an Assistant Professor in Biochemistry at the Department of Chemistry and Biochemistry at the University of Texas. Arlington. While teaching Biochemistry, I developed more than a hobby like interest in using structure viewers as educational tools. I began incorporating the latest developments in my Biochemistry classes. I taught Biological Chemistry, for the University of Maryland, Baltimore County. My students were required to learn how to use a structure viewer and explore properties of proteins using the viewer and other web based tools. After a stint with Smithsonian Institution, NIH and Army Forensic Unit, I am happily employed at Georgia Gwinnett College teaching chemistry and biochemistry.
*[[User:Tom Gluick/Snadbox1]]

User:Tom Gluick/Snadbox1

2011-09-23T20:20:52Z

Tom Gluick: Nema MENIN Structure

NEma MENIN Structure

User:Tom Gluick

2011-09-23T20:16:59Z

Tom Gluick:

<nowiki><nowiki>Insert non-formatted text here</nowiki></nowiki>I earned a Ph.D. in Chemistry in 1980 from the Chemistry Department of the University of Montana. After a lengthy prodoctoral stint at Johns Hopkins Unviersity, I was an Assistant Professor in Biochemistry at the Department of Chemistry and Biochemistry at the University of Texas. Arlington. While teaching Biochemistry, I developed more than a hobby like interest in using structure viewers as educational tools. I began incorporating the latest developments in my Biochemistry classes. I taught Biological Chemistry, for the University of Maryland, Baltimore County. My students were required to learn how to use a structure viewer and explore properties of proteins using the viewer and other web based tools. Because of budget cuts in the UM system, adjunct faculty were not rehired, so I am on biochemistry teaching hiatus. I hope to teach Biological Chemistry again.
*[[User:Tom Gluick/Snadbox1]]

Proteopedia:Page of the Year Entrants

2009-12-31T20:24:07Z

Tom Gluick:

Please list your entry in [[Proteopedia:Page of the Year Competition| Proteopedia's Page of the Year Competition]] here. You can enter as many pages as you like.
Add your entry to the list by adding a row in the format shown below, with a link to your user page followed by 2 hyphens and then a link to the page you're entering in the competition.

----

==Entrants==

Entry number 1 is just an example, Eran cannot participate in the competition.

# [[User:Eran Hodis]] -- [[User:Eran_Hodis/Acetylcholinesterase]]
# [[User:Ramiro Barrantes]] -- [[1tdh]]
# [[User:Sara Toftegaard Petersen]] [[User:Mathilde Thomsen]] [[User:Mette Trauelsen]] -- [[Nitric oxide synthase]]
# [[User:Wayne Decatur]] -- [[Ribosome]] (see history for original article as of October 15, 2009)
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
# [[User:Tzviya Zeev-Ben-Mordehai]] -- [[Intrinsically Disordered Protein]] (see history for original article as of October 19, 2009)
# [[User:Tilman Schirmer]] -- [[C-di-GMP signaling]] (Note that there are several sub-pages)
# [[User:Joseph Lipsick]] -- [[SRC]]
# [[User:Joseph Lipsick]] -- [[Ras]]
# [[User:Maitreyee Mukherjee]] -- [[PHB synthase in Rhodobacter sphaeroides]]
# [[User:Paula Grabowski]] -- [[Triosephosphate Isomerase]]
# [[User:Céline Debarnot]] -- [[sandbox123]]
# [[User:Gregg Snider]] -- [[Triose Phosphate Isomerase]]
# [[User:Yash Patankar]] -- [[User:Yash Patankar/Sandbox 1]]
# [[User:Julien Madouasse]] -- [[SAndbox 159]]
# [[User:Mkukrishna]] -- [[E.COLI OMPC - CAMEL LACTOFERRIN COMPLEX]]
# [[User:Lois_A._Fridmann]] -- [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
# [[User:Lois_A._Fridmann]] -- [[User:Lois A. Fridmann/Sandbox 1]]
# [[User:Lois_A._Fridmann]] -- [[User:Lois A. Fridmann/Sandbox 2]]
# [[User:Jianlin Cheng]] -- [[1gwp]]
# [[User:Nicolas Villanueva]] -- [[NS5B]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]]
# [[User:Daniel Seeman]] -- [[Alpha-1-antitrypsin]] (has an NMR format pdb in it, takes a while to load)
# [[User:Michael Strong]] -- [[2g38]]
# [[User:Michael Strong]] -- [[User:Michael_Strong/H1N1]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit]]
# [[User:Tom Gluick]] -- [[User:Tom Gluick/glutamine synthetase]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Interactions between Antibiotics and the Ribosome]]
# [[User:Wayne Decatur]] -- [[User:Wayne_Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin]]

Proteopedia:Page of the Year Entrants

2009-12-31T02:22:49Z

Tom Gluick: /* Entrants */

Please list your entry in [[Proteopedia:Page of the Year Competition| Proteopedia's Page of the Year Competition]] here. You can enter as many pages as you like.
Add your entry to the list by adding a row in the format shown below, with a link to your user page followed by 2 hyphens and then a link to the page you're entering in the competition.

----

==Entrants==

Entry number 1 is just an example, Eran cannot participate in the competition.

# [[User:Eran Hodis]] -- [[User:Eran_Hodis/Acetylcholinesterase]]
# [[User:Ramiro Barrantes]] -- [[1tdh]]
# [[User:Sara Toftegaard Petersen]] [[User:Mathilde Thomsen]] [[User:Mette Trauelsen]] -- [[Nitric oxide synthase]]
# [[User:Wayne Decatur]] -- [[Ribosome]] (see history for original article as of October 15, 2009)
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
# [[User:Tzviya Zeev-Ben-Mordehai]] -- [[Intrinsically Disordered Protein]] (see history for original article as of October 19, 2009)
# [[User:Tilman Schirmer]] -- [[C-di-GMP signaling]] (Note that there are several sub-pages)
# [[User:Joseph Lipsick]] -- [[SRC]]
# [[User:Joseph Lipsick]] -- [[Ras]]
# [[User:Maitreyee Mukherjee]] -- [[PHB synthase in Rhodobacter sphaeroides]]
# [[User:Paula Grabowski]] -- [[Triosephosphate Isomerase]]
# [[User:Céline Debarnot]] -- [[sandbox123]]
# [[User:Gregg Snider]] -- [[Triose Phosphate Isomerase]]
# [[User:Yash Patankar]] -- [[User:Yash Patankar/Sandbox 1]]
# [[User:Julien Madouasse]] -- [[SAndbox 159]]
# [[User:Mkukrishna]] -- [[E.COLI OMPC - CAMEL LACTOFERRIN COMPLEX]]
# [[User:Lois_A._Fridmann]] -- [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
# [[User:Lois_A._Fridmann]] -- [[User:Lois A. Fridmann/Sandbox 1]]
# [[User:Lois_A._Fridmann]] -- [[User:Lois A. Fridmann/Sandbox 2]]
# [[User:Jianlin Cheng]] -- [[1gwp]]
# [[User:Nicolas Villanueva]] -- [[NS5B]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]]
# [[User:Daniel Seeman]] -- [[Alpha-1-antitrypsin]] (has an NMR format pdb in it, takes a while to load)
# [[User:Michael Strong]] -- [[2g38]]
# [[User:Michael Strong]] -- [[User:Michael_Strong/H1N1]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit]]
# [[User:Tom Gluick]] -- [[User:Tom Gluick/Human Glutamine Synthetase]]
# [[User:Tom Gluick]] -- [[User:Tom Gluick/glutamine synthetase]]

Proteopedia:Page of the Year Entrants

2009-12-31T02:21:42Z

Tom Gluick: /* Entrants */

Please list your entry in [[Proteopedia:Page of the Year Competition| Proteopedia's Page of the Year Competition]] here. You can enter as many pages as you like.
Add your entry to the list by adding a row in the format shown below, with a link to your user page followed by 2 hyphens and then a link to the page you're entering in the competition.

----

==Entrants==

Entry number 1 is just an example, Eran cannot participate in the competition.

# [[User:Eran Hodis]] -- [[User:Eran_Hodis/Acetylcholinesterase]]
# [[User:Ramiro Barrantes]] -- [[1tdh]]
# [[User:Sara Toftegaard Petersen]] [[User:Mathilde Thomsen]] [[User:Mette Trauelsen]] -- [[Nitric oxide synthase]]
# [[User:Wayne Decatur]] -- [[Ribosome]] (see history for original article as of October 15, 2009)
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Plant Viral Protein p19 Suppression of RNA Silencing]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Suppression of RNA Silencing by Viruses]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Tomato aspermy virus protein 2b Suppression of RNA Silencing]]
# [[User:Tzviya Zeev-Ben-Mordehai]] -- [[Intrinsically Disordered Protein]] (see history for original article as of October 19, 2009)
# [[User:Tilman Schirmer]] -- [[C-di-GMP signaling]] (Note that there are several sub-pages)
# [[User:Joseph Lipsick]] -- [[SRC]]
# [[User:Joseph Lipsick]] -- [[Ras]]
# [[User:Maitreyee Mukherjee]] -- [[PHB synthase in Rhodobacter sphaeroides]]
# [[User:Paula Grabowski]] -- [[Triosephosphate Isomerase]]
# [[User:Céline Debarnot]] -- [[sandbox123]]
# [[User:Gregg Snider]] -- [[Triose Phosphate Isomerase]]
# [[User:Yash Patankar]] -- [[User:Yash Patankar/Sandbox 1]]
# [[User:Julien Madouasse]] -- [[SAndbox 159]]
# [[User:Mkukrishna]] -- [[E.COLI OMPC - CAMEL LACTOFERRIN COMPLEX]]
# [[User:Lois_A._Fridmann]] -- [[HIV-1 Gag Recruitment of Tsg101 and the Viral Budding Process]]
# [[User:Lois_A._Fridmann]] -- [[User:Lois A. Fridmann/Sandbox 1]]
# [[User:Lois_A._Fridmann]] -- [[User:Lois A. Fridmann/Sandbox 2]]
# [[User:Jianlin Cheng]] -- [[1gwp]]
# [[User:Nicolas Villanueva]] -- [[NS5B]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Flock house virus B2 protein Suppression of RNA Silencing]]
# [[User:Daniel Seeman]] -- [[Alpha-1-antitrypsin]] (has an NMR format pdb in it, takes a while to load)
# [[User:Michael Strong]] -- [[2g38]]
# [[User:Michael Strong]] -- [[User:Michael_Strong/H1N1]]
# [[User:Wayne Decatur]] -- [[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit]]
# [[User:Tom Gluick]] -- [[User:Tom Gluick/Human Glutamine Synthetase]]
# [[User:Tom Gluick]] -- [[User:Tom Gluick/Glutamine Synthetase]]

User:Tom Gluick/Human Glutamine Synthetase

2009-12-31T02:17:07Z

Tom Gluick: /* Quaternary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_strcuture_spacefill/1'> its adjacent subunits in the same ring, and with two subunits below the ring.</scene> One notices that the quaternary interactions of one subunit involves half the complex, and that the contacts between Chain A with either E or B are extensive, but those with F or G are much fewer in comparison. 

In the subpages that follow[[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]], a more extensive view of the subunit interactions is given. The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase/Quaternary Structure

2009-12-31T02:14:18Z

Tom Gluick: /* Quaternary Structure */

==Quaternary Structure==
<applet load='2qc8' size='700' frame='true' align='center' caption='Quaternary Structure Display' /> 
The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising of hydrogen bonds and noncovalent interactions. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>
 

<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_Structure/Quaternary_structure_ab/1'>TextToBeDisplayed</scene>

Proteopedia:Page of the Year Entrants

2009-12-31T02:07:41Z

Tom Gluick:

Proteopedia:Page of the Year Entrants

2009-12-31T02:02:04Z

Tom Gluick: /* Entrants */

User:Tom Gluick

2009-12-31T01:49:46Z

Tom Gluick:

I earned a Ph.D. in Chemistry in 1980 from the Chemistry Department of the University of Montana. After a lengthy prodoctoral stint at Johns Hopkins Unviersity, I was an Assistant Professor in Biochemistry at the Department of Chemistry and Biochemistry at the University of Texas. Arlington. While teaching Biochemistry, I developed more than a hobby like interest in using structure viewers as educational tools. I began incorporating the latest developments in my Biochemistry classes. I taught Biological Chemistry, for the University of Maryland, Baltimore County. My students were required to learn how to use a structure viewer and explore properties of proteins using the viewer and other web based tools. Because of budget cuts in the UM system, adjunct faculty were not rehired, so I am on biochemistry teaching hiatus. I hope to teach Biological Chemistry again.

User:Tom Gluick/Human Glutamine Synthetase/Quaternary Structure

2009-01-20T02:42:03Z

Tom Gluick: /* Quaternary Structure */

==Quaternary Structure==
<applet load='2qc8' size='700' frame='true' align='center' caption='Quaternary Structure Display' /> 
The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>
 

<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_Structure/Quaternary_structure_ab/1'>TextToBeDisplayed</scene>

User:Tom Gluick/Human Glutamine Synthetase/Quaternary Structure

2009-01-20T02:39:09Z

Tom Gluick: /* Quaternary Structure */

==Quaternary Structure==
<applet load='2qc8' size='700' frame='true' align='center' caption='Quaternary Structure Display' /> 
The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>
 

<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_structure_ab/1'>TextToBeDisplayed</scene>

User:Tom Gluick/Human Glutamine Synthetase/Quaternary Structure

2009-01-18T21:20:31Z

Tom Gluick: /* Quaternary Structure */

==Quaternary Structure==
<applet load='2qc8' size='700' frame='true' align='center' caption='Quaternary Structure Display' /> 
The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

User:Tom Gluick/Human Glutamine Synthetase/Quaternary Structure

2009-01-18T21:19:28Z

Tom Gluick: /* Quaternary Structure */

==Quaternary Structure==
<applet load='2qc8' size='700' frame='true' align='center' caption='Quaternary Structure Display' /> 
The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

User:Tom Gluick/Human Glutamine Synthetase/Quaternary Structure

2009-01-18T21:17:52Z

Tom Gluick: /* Quaternary Structure */

==Quaternary Structure==
<applet load='2qc8' size='700' frame='true' align='center' caption='Quaternary Structure Display' />

User:Tom Gluick/Human Glutamine Synthetase/Quaternary Structure

2009-01-18T21:14:16Z

Tom Gluick: New page: ==Quaternary Structure== <applet load='2qc8' size='800' frame='true' align='center' caption='Quaternary Structure Display' />

==Quaternary Structure==
<applet load='2qc8' size='800' frame='true' align='center' caption='Quaternary Structure Display' />

User:Tom Gluick/Human Glutamine Synthetase

2009-01-18T21:11:35Z

Tom Gluick: /* Quaternary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_strcuture_spacefill/1'>its adjacent subunits in the same ring, and with two subunits below the ring.</scene> One notices that the quaternary interactions of one subunit involves half the complex, and that the contacts between Chain A with either E or B are extensive, but those with F or G are much fewer in comparison. 

In the subpages that follow[[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]], a more extensive view of the subunit interactions is given. The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-18T21:10:14Z

Tom Gluick: /* Quaternary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_strcuture_spacefill/1'>its adjacent subunits in the same ring, and with two subunits below the ring.</scene> One notices that the quaternary interactions of one subunit involves half the complex, and that the contacts between Chain A with either E or B are extensive, but those with F or G are much fewer in comparison. 

In the subpages that follow[[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]], a more extensive view of the subunit interactions is given. The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. [[User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary Structure]] Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-18T21:07:57Z

Tom Gluick: /* Quaternary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_strcuture_spacefill/1'>its adjacent subunits in the same ring, and with two subunits below the ring.</scene> One notices that the quaternary interactions of one subunit involves half the complex, and that the contacts between Chain A with either E or B are extensive, but those with F or G are much fewer in comparison. 

In the subpages that follow, a more extensive view of the subunit interactions is given. The <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>amino acid residues involved in quaternary interactions between subunit A and subunit B</scene> are very extensive comprising a ## fraction of the entire surface area of the subunit. Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-18T21:05:06Z

Tom Gluick: /* Quaternary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_strcuture_spacefill/1'>its adjacent subunits in the same ring, and with two subunits below the ring.</scene> One notices that the quaternary interactions of one subunit involves half the complex, and that the contacts between Chain A with either E or B are extensive, but those with F or G are much fewer in comparison. 

In the subpages that follow, a more extensive view of the subunit interactions is given. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User talk:Eran Hodis

2009-01-18T21:02:45Z

Tom Gluick: /* Moving scenes from one page to another */

==News from Greece==
Hi Eran,
actually I was on vacation after the summer school of Erice!
The last days I'm back in the lab and try to find the rythm of the experiments ;)
I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.
We'll be in contact..you'll see the progress of my page!

best wishes
Maria
---------

Hi Eran,
Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.
best regards
Trevor
---------

== Bad green link ==
Eran,
I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?

Karl

---------
After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.

Karl

== PDBsum site ==
Eran,
After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.

By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.

Karl

Eran,
I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.

Karl

== Proteopedia for teaching ==
Hi Eran

I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:

1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)

2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.

cheers!

Shaun

== What to do with my students contributions ==

Hi Eran,

I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?

Tom

== Surfaces ==

Hi Eran,

I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.

Tom

== more on surfaces ==

Hi

Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces. 
my best 
Tom 
PS. So, what is the Israeli greetings/salutation during Hannukah?

== Cheers Eran! ==

Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific.

BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)

== RE: ==

Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST)

: With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)

:: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)

==RE: Models==

Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!

== Moving scenes from one page to another ==

Hi Eran,

I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <nowiki><scene>...<scene/></nowiki> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.

Tom

User talk:Eran Hodis

2009-01-18T21:01:48Z

Tom Gluick: Moving scenes from one page to another

==News from Greece==
Hi Eran,
actually I was on vacation after the summer school of Erice!
The last days I'm back in the lab and try to find the rythm of the experiments ;)
I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.
We'll be in contact..you'll see the progress of my page!

best wishes
Maria
---------

Hi Eran,
Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.
best regards
Trevor
---------

== Bad green link ==
Eran,
I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?

Karl

---------
After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.

Karl

== PDBsum site ==
Eran,
After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.

By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.

Karl

Eran,
I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.

Karl

== Proteopedia for teaching ==
Hi Eran

I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:

1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)

2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.

cheers!

Shaun

== What to do with my students contributions ==

Hi Eran,

I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?

Tom

== Surfaces ==

Hi Eran,

I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.

Tom

== more on surfaces ==

Hi

Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces. 
my best 
Tom 
PS. So, what is the Israeli greetings/salutation during Hannukah?

== Cheers Eran! ==

Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific.

BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)

== RE: ==

Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST)

: With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)

:: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)

==RE: Models==

Thanks Eran! We have been busier than expected at the CBM (but what else is new). Still, we hope to continue working on Proteopedia to upload more and more images of models we have developed - as well as some working SMART Team pages. Joel let me know that all the models made it to him intact so he should have them to show off when he gets back on your side of the world. It is a pretty neat collection of a very interesting topic - so enjoy!

== Moving scenes from one page to another ==

Hi Eran,

I am able to copy wiki script from one page and copy it to another page using copy command: I can do ths copy <scene>...<scene/> (assuming I wrote the syntax correctly) from User:Tom Gluick/Human Glutamine Synthetase (section) to User:Tom Gluick/Human Glutamine Synthetase (section)/quaternary a subpage. However, I would like to change the scene in the subpage, but when SAT is access in subpage, the scene is not found associated with the subpage. is there something that can be done to remedy this issue. It would certainly save me time if this were possible.

Tom

User:Tom Gluick/Human Glutamine Synthetase

2009-01-17T22:02:58Z

Tom Gluick: /* Quaternary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Quaternary_strcuture_spacefill/1'>its adjacent subunits in the same ring, and with two subunits below the ring.</scene> One notices that the quaternary interactions of one subunit involves half the complex, and that the contacts between Chain A with either E or B are extensive, but those with F or G are much fewer in comparison <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase/Large Image Showing Signature with labels

2009-01-17T03:40:05Z

Tom Gluick: /* Gln A Synthetase Signature */

==Gln A Synthetase Signature==
<applet load='2qc8' size='600' frame='true' align='center' caption='Signature' />
<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/A_domain/3'>TextToBeDisplayed</scene>

User:Tom Gluick/Human Glutamine Synthetase/Large Image Showing Signature with labels

2009-01-17T03:37:02Z

Tom Gluick: New page: ==Gln A Synthetase Signature== <applet load='2qc8' size='600' frame='true' align='center' caption='Signature' />

==Gln A Synthetase Signature==
<applet load='2qc8' size='600' frame='true' align='center' caption='Signature' />

User:Tom Gluick/Human Glutamine Synthetase

2009-01-17T03:33:50Z

Tom Gluick: /* Primary Structure and Catalytic Residues */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-17T03:16:25Z

Tom Gluick: /* Primary Structure and Catalytic Residues */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[Tom Gluick/Human Glutamine Synthetase/Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

Large Image Showing Signature with labels

2009-01-17T02:58:03Z

Tom Gluick: /* GLNA signature */

==GLNA signature==

<applet load='2qc8' size='700' frame='true' align='center' caption='Insert caption here' />

put stufff here.
<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/A_domain/3'>TextToBeDisplayed</scene>

Large Image Showing Signature with labels

2009-01-17T02:50:51Z

Tom Gluick: /* GLNA signature */

==GLNA signature==

<applet load='2qc8' size='700' frame='true' align='center' caption='Insert caption here' />

put stufff here.

Large Image Showing Signature with labels

2009-01-17T02:46:36Z

Tom Gluick: New page: ==GLNA signature== Replace the PDB id after the STRUCTURE_ and after PDB= to load and display another structure. {{STRUCTURE_2qc8 | PDB=2qc8 | SCENE= }}

==GLNA signature==

Replace the PDB id after the STRUCTURE_ and after PDB= to load
and display another structure.

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

User:Tom Gluick/Human Glutamine Synthetase

2009-01-17T02:45:25Z

Tom Gluick: /* Primary Structure and Catalytic Residues */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)] The view shows a space-fill model similar to the one shown in prosite. A larger view showing the labeled residues with the signature is shown in this link[[Large Image Showing Signature with labels]].

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-17T02:41:06Z

Tom Gluick: /* Enzyme Active Site */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)]

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 
 
===Disease State===

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-17T01:59:00Z

Tom Gluick: /* Primary Structure and Catalytic Residues */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1)]

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-16T17:17:50Z

Tom Gluick: /* Primary Structure and Catalytic Residues */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

Gln A signatures from analysis--select 62-79A or 62-79C or 62-79D or 62-79B or 62-79E rasmol command; see[http://http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 Prosite PS00180 (GLNA_1]

Glutamine synthetase putative ATP binding site determined from analysis is [http://www.expasy.org/cgi-bin/prosite-search-ac?PDOC00162 ATP binding regions PS00181 select 241-257A or 241-257C or 241-257D or 241-257B or 241-257E]

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-14T18:34:53Z

Tom Gluick: /* Secondary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

===Primary Structure and Catalytic Residues===

===Enzyme Active Site===
It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-14T18:30:13Z

Tom Gluick: /* Tertiary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

===Secondary Structure===
The composed of --- alpha helices<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_alpha/1'>alpha helices</scene>in pink, ----beta strands<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_beta/1'>beta strands</scene>in green, ---- and various types of turns<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Secondary_remaining/1'>turns and random coil regions</scene>in white. The wiring diagram shown in PDBsum shows the secondary structure elements in an easily understood format.

It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-11T03:44:01Z

Tom Gluick: /* Tertiary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
Each tertiary structure of each subunit consists ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>Two Domains</scene>; the red domain is ; and the blue domain is...
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-11T03:29:03Z

Tom Gluick: /* Tertiary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
the protein is ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>TextToBeDisplayed</scene>
alpha beta
two domains
Catalytic domain--c- terminal 
beat grasp domain. n-terminal

 

It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-10T23:03:01Z

Tom Gluick: /* Tertiary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
the protein is ...<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Tertiary_structure_both_domain/1'>TextToBeDisplayed</scene>
alpha beta
two domains
Catalytic domain--110-363
other domain.

 

It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-10T19:49:40Z

Tom Gluick: /* Tertiary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
the protein is ...
alpha beta
two domains
Catalytic domain
other domain.

 

It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-10T19:32:25Z

Tom Gluick: /* Tertiary Structure */

==Practice Page for Human Glutamine Synthetase==
{{STRUCTURE_2qc8| PDB= 2qc8 | SCENE= }} 
Glutamine synthetase is a key component in the regulation of the concentration of nitrogen containing compounds through out the phyla. The enzyme synthesizes glutamine from glutamate, ATP, and ammonium ion via a two step mechanism involving an glutamyl-P intermediate. The ATP provides the driving force for the reaction by esterifying glutamate's C-3 carboxyl group with the γ-phosphate that is later displaced by ammonia. Glutamine is incorporated into proteins, serves as an energy source, is involved in assimilating ammonia to be used in amino acid and nucleic acid synthesis. 

===Quaternary Structure===
The quaternary structure consists of ten identical subunits arranged as two pentameric rings stacked atop each other [http://www.ebi.ac.uk/pdbsum/2d3b] as shown in the Java Applet on the right hand side of the page. Each subunit makes interacts with its adjacent subunits in the same ring, and with two subunits below the ring. <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Hydrogen_bond_a_and_b_and_ha_h/1'>Residues involved in quaternary interactions between subunit A and subunit B on the same ring</scene> Interactions between subunit A and E is shown <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Surface_a_and_surface_e/2'>Quaternary interactions between subunit A and E</scene> Quaternary interactions between subunit A to subunit F <scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_to_subunit_f/1'>Quaternary contacts between A and F</scene>or to subunit G on the other ring.<scene name='User:Tom_Gluick/Human_Glutamine_Synthetase/Subunit_a_and_subunit_g/1'>TextToBeDisplayed</scene>

===Tertiary Structure===
the protein is ...

 

It is activated by Mn and several other divalent metal cations and α-keotglutarate; the enzyme is inhibited by methionine sulfoxime, glycine and carbamoyl phosphate.<ref>Haussinger, D., & Schleiss, F., Glutamine metabolism and signaling in the liver, Forntiers in Bioscience 2007, 12, 371-391.</ref> 

Glutamine synthetase is a key component in controlling ammonia concentrations, maintaining nitrogen balance among organs, acid-base homeostasis, gene regulation and signaling.<ref> Curi, R., Glutamine, gene expression, and cell function. Frontiers in Bioscience 2007 12: 344-357. </ref> Glutamine homeostasis is maintained in part via regulating transcription and GS protein degradation. <ref> Labow, B. I., ''et.al.'', Mechanisms Governing the Expression of the Enzymes of Glutamine
Metabolism—Glutaminase and Glutamine Synthetase. J. Nutr. 2001 131: 2467S–2474S.</ref>.
In ureoteles, glutamine serves as a nontoxic shuttle of excess ammonia as its transported from tissues not capable of processing ammonia further through the blood to the liver where amide nitrogen eventually ends up in urea. For neurons in the brain to function normally, the excititory glutamate generated by the neuron is absorbed by the astrocyte and recycled to glutamine by GS.<ref> Albrecht, J., Glutamine in the central nervous system: function and dysfunction. Frontiers in Bioscience 2007 12:332-343. </ref>
Disruptions in glutamine homeostasis brought about through cancer, trauma or HiV infection can lead to organ failure and death. Although extremely rare and only seen in the children of consnaguionoius couples, that defects in GLUL ( the gene encoding for gluatmine synthetase) causes a congenital disorder leading to brain malformation and death in neonates[http://ca.expasy.org/cgi-bin/niceprot.pl?P15104].<ref>Haberle, J., ''et.al.'', Congenital Glutamine Deficiency with Glutamine Synthetase Mutations. New Engl J Med 2003 353:1926-33.</ref>
 

Below the cartoon shown in the JMOL applet is a wealth of information linked to this site. Links immediately below provide views of ligands associated with the protein. Click on ADP or any other ligand in the green region will show cause the protein to become transparent revealing the buried ligand. Clicking on green link initial scene will return the image to the original scene. More information about the structure is found in the human glutamine synthetase stub[http://www.proteopedia.org/wiki/index.php/2qc8] and references sited therein. This information can be also accessed by clicking the PFAM links in structural annotation resources. Clicking on the domains reveals the CCD database complied by NCBI. Images of the two GS domains can be visualized using this link. PDBsum and the RCSB links provide complementary information on ligand-protein interactions, protein-protein contacts, and literature citations as well as providing links to other resources.
 

Before you start the project, I suggest you view the video tutorial in [http://www.proteopedia.org/wiki/index.php/Proteopedia:Video_Guide] to provide you with the tools to get started and give you a great overview of the power of proteopedia. I also suggest that you be aware of scene authoring tools with detailed explanations link given in[http://proteopedia.org/wiki/index.php/Scene_authoring_tools] and the editing page access in Help.

==References==
<references/>

User:Tom Gluick/Human Glutamine Synthetase

2009-01-10T19:29:53Z

Tom Gluick: /* Practice Page for Human Glutamine Synthetase */

User:Tom Gluick/Human Glutamine Synthetase

2009-01-10T03:54:27Z

Tom Gluick: /* Practice Page for Human Glutamine Synthetase */