Sandbox Reserved 1065: Difference between revisions

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{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->*[[User:Isaac C. Gluesenkamp/Sandbox 1]]
==Your Protein Name here==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>Zinc Dependent MarR Family Transcriptional Regulator AdcR
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; 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.


== Biological Function ==


==Your Heading Here (maybe something like 'Structure')==
== Structural Overview ==


<StructureSection load='3r44' size='340' side='right' caption='Very Long Chain Fatty Acyl CoA Synthetase (FadD13)' scene='69/694232/Opening_scene/1'>
== Mechanism of Action ==


== General mechanism for the activation of fatty acids ==
== Zinc Ligand(s) ==
FadD13 first activates the fatty acid through a reaction with ATP to form an acyl adenylate intermediate and release pyrophosphate. Following a conformational change of the enzyme, coenzyme A is able to bind and reaction with the acyl adenylate intermediate forming the acyl CoA product (Figure 1).


=active site (to be copied over)=
== Other Ligands ==
 
A high conserved residue in the C-terminal region, <scene name='69/694233/Lys_487/2'>Lysine 487</scene>, resulted in a 95% loss of function of FadD13 and is thought to be involved in the orientation of the substrates to form the adenylate intermediate.<ref name="residue paper">PMID: 20027301</ref> Other mutation studies, found that Serine 404 was involved in the binding of Coenzyme A which may only occur once the region incurs a 140 degree rotational change.<ref name="Our Paper"/><ref name="residue paper"/>
 
 
 
 
== Function ==
 
 
This is the <scene name='69/694232/Arginine_rich_lid_loop/1'>Arginie-rich lid loop</scene>.<ref name="OUR PAPER">PMID: 22560731</ref>
 
This is the <scene name='69/694232/Linker_section/2'>linker</scene>.<ref name="OUR PAPER"/>
 
FadD13 has three different <scene name='69/694232/Domains/2'>regions</scene>: The N-terminal region (1-395) is in blue, the C-terminal region (402-403) is in red, and the six amino acid linker is in tan (citation for original paper).
 
The adenine of ATP is bound to a group of <scene name='69/694232/Adenine_binding_group/2'>six amino acids (300-305)</scene> that is structurally identically to other acyl-CoA synthetases (Citation for original paper).
 
citation 1 <ref name="Our Paper">PMID: 22560731</ref>
<ref name="OUR PAPER"/>
 
citation 2 <ref name="JT">PMID: 20454815</ref>
<ref name="JT"/>
 
Citation 3 <ref name="SM">PMID: 12164478</ref>
<ref name="SM"/>
 
 
== 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.
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.

Latest revision as of 21:38, 3 March 2017

This Sandbox is Reserved from 02/09/2015, through 05/31/2016 for use in the course "CH462: Biochemistry 2" taught by Geoffrey C. Hoops at the Butler University. This reservation includes Sandbox Reserved 1051 through Sandbox Reserved 1080.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
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More help: Help:Editing

*User:Isaac C. Gluesenkamp/Sandbox 1

Your Protein Name hereYour Protein Name here

Zinc Dependent MarR Family Transcriptional Regulator AdcR

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 [1] or to the article describing Jmol [2] to the rescue.

Biological Function

Structural Overview

Mechanism of Action

Zinc Ligand(s)

Other Ligands

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.


Caption for this structure

Drag the structure with the mouse to rotate

ReferencesReferences

  1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA, Joseph Thomas, Geoffrey C. Hoops, Isaac C. Gluesenkamp
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