Sandbox Reserved 338

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 5: Line 5:
{{STRUCTURE_2vnc | PDB=2vnc | SCENE=Sandbox_Reserved_338/2vnc/1}}
{{STRUCTURE_2vnc | PDB=2vnc | SCENE=Sandbox_Reserved_338/2vnc/1}}
-
A debranching enzyme is responsible for the breakdown of glycogen <ref name="Woo"> PMID:18703518 </ref>. There are two main groups of debranching enzymes, and they are separated according to their activity <ref name="Woo" />. The first group, consisting of [http://en.wikipedia.org/wiki/Pullulanase pullulanase] and isoamylases which only possess one function α-1,6-glycosidase activity <ref name="Woo" />. Whereas the second group consists of glycogen debranching enzymes which possess two functions, both α-1,6-glycosidase and α-1,4-transferase activity <ref name="Woo" />.
+
==Introduction==
 +
A debranching enzyme is responsible for the breakdown of glycogen <ref name="Woo">PMID: 18703518 </ref>. There are two main groups of debranching enzymes, and they are separated according to their activity <ref name="Woo" />. The first group, consists of pullulanases and isoamylases which only exhibit α-1,6-glycosidase activity <ref name="Woo" />. Whereas the second group consists of glycogen debranching enzymes which possess two functions; both α-1,6-glycosidase and α-1,4-transferase activity <ref name="Woo" />.
 +
TreX is an archaeal glycogen debranching enzyme from the species, ''Sulfolobus solfataricus'' <ref name="Woo" />. Even though TreX exhibits 74% sequence similarity to the isoamylase from ''Sulfolobus acidocaldarium'', TreX itself exhibits both α-1,6-glycosidase and α-1,4-transferase activity <ref name="Woo" />. It functions to debranch the side chains of glycogen into maltodextrin, and subsequently TreY and TreZ convert the maltodextrin into trehalose <ref name="Woo" /> <ref name="Park"> doi:10.1080/10242420701806652 </ref>. TreX can be found in two oligomeric states, either as a dimer or as a tetramer. As TreX is an oligomer, each conformational state exhibits a different catalytic activity <ref name="Woo" />.
 +
there is a glutamate residue, <scene name='Sandbox_Reserved_338/2vnc/3'>residue 100</scene> that I am interested in showing.
there is a glutamate residue, <scene name='Sandbox_Reserved_338/2vnc/3'>residue 100</scene> that I am interested in showing.
 +
 +
==Structure and Function==
 +
TreX is an oligomer, as it exists in a dimeric state and a tetrameric state, both of which are active in solution <ref name="Woo" />. All subunits are identical, where the monomer contains 612 amino acids in total <ref name="Woo" />. The polypeptide folds into two secondary structures, a β-sandwhich in the N terminal region, comprised of six β-strands and a (β/α)8 – barrel motif in the central domain, comprised of eight parallel α-strands which encircle eight parallel β-strands <ref name="Woo" />. The sequence composition of the TreX monomer exhibits a high degree of homology to the isoamylase debranching enzyme of Pseudomona, however the TreX monomer mainly deviates from this similarity in its substrate binding groove and the absence of a calcium ion ligand <ref name="Woo" />.
 +
 +
In the dimeric form, the individual subunits are adjacent to each other, where both of the active sites face the same side <ref name="Woo" />. In the tetrameric form, two of the associated dimers face each other so as to position the active sites on the inside of the tetramer <ref name="Woo" />.
 +
 +
More to come…
 +
 +
==Mechanism==
==References==
==References==
<references/>
<references/>

Revision as of 02:30, 17 March 2011

This Sandbox is Reserved from January 10, 2010, through April 10, 2011 for use in BCMB 307-Proteins course taught by Andrea Gorrell at the University of Northern British Columbia, Prince George, BC, Canada.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
  • Click the 3D button (when editing, above the wikitext box) to insert Jmol.
  • show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
  • Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing


PDB ID 2vnc

Drag the structure with the mouse to rotate
2vnc, resolution 3.00Å ()
Related: 2vuy, 2vr5, 2vnb
Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml



Contents

Introduction

A debranching enzyme is responsible for the breakdown of glycogen [1]. There are two main groups of debranching enzymes, and they are separated according to their activity [1]. The first group, consists of pullulanases and isoamylases which only exhibit α-1,6-glycosidase activity [1]. Whereas the second group consists of glycogen debranching enzymes which possess two functions; both α-1,6-glycosidase and α-1,4-transferase activity [1].

TreX is an archaeal glycogen debranching enzyme from the species, Sulfolobus solfataricus [1]. Even though TreX exhibits 74% sequence similarity to the isoamylase from Sulfolobus acidocaldarium, TreX itself exhibits both α-1,6-glycosidase and α-1,4-transferase activity [1]. It functions to debranch the side chains of glycogen into maltodextrin, and subsequently TreY and TreZ convert the maltodextrin into trehalose [1] [2]. TreX can be found in two oligomeric states, either as a dimer or as a tetramer. As TreX is an oligomer, each conformational state exhibits a different catalytic activity [1].


there is a glutamate residue, that I am interested in showing.

Structure and Function

TreX is an oligomer, as it exists in a dimeric state and a tetrameric state, both of which are active in solution [1]. All subunits are identical, where the monomer contains 612 amino acids in total [1]. The polypeptide folds into two secondary structures, a β-sandwhich in the N terminal region, comprised of six β-strands and a (β/α)8 – barrel motif in the central domain, comprised of eight parallel α-strands which encircle eight parallel β-strands [1]. The sequence composition of the TreX monomer exhibits a high degree of homology to the isoamylase debranching enzyme of Pseudomona, however the TreX monomer mainly deviates from this similarity in its substrate binding groove and the absence of a calcium ion ligand [1].

In the dimeric form, the individual subunits are adjacent to each other, where both of the active sites face the same side [1]. In the tetrameric form, two of the associated dimers face each other so as to position the active sites on the inside of the tetramer [1].

More to come…

Mechanism

References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 Woo EJ, Lee S, Cha H, Park JT, Yoon SM, Song HN, Park KH. Structural insight into the bifunctional mechanism of the glycogen-debranching enzyme TreX from the archaeon Sulfolobus solfataricus. J Biol Chem. 2008 Oct 17;283(42):28641-8. Epub 2008 Aug 14. PMID:18703518 doi:10.1074/jbc.M802560200
  2. ↑ doi: https://dx.doi.org/10.1080/10242420701806652
Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_338"
Personal tools