Sandbox Reserved 338

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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.

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spinqualitylabelsall models PDB ID 2vnc Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image
2vnc, resolution 3.00Å ()
Related:	2vuy, 2vr5, 2vnb
Structural annotation: Resources: InterPro : Ipr017853, Ipr013780, Ipr015902, Ipr014756, Ipr013783, Ipr013781, Ipr011837, Ipr006047, Ipr004193 Pfam : PF00128, PF02922
Evolutionary conservation: Toggle Conservation Colors: Rows = identical sequences: Further Information: Caveats, Explanation, Complete Results at ConSurfDB
Resources:	FirstGlance, OCA, RCSB, PDBsum
Coordinates:	save as pdb, mmCIF, xml

Contents 1 Introduction 2 Structure and Function 3 Mechanism 4 References

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].

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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

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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