This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1ll2

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1ll2" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ll2, resolution 1.9&Aring;" /> '''Crystal Structure of ...)
Current revision (07:33, 14 February 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ll2.gif|left|200px]]<br /><applet load="1ll2" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1ll2, resolution 1.9&Aring;" />
 
-
'''Crystal Structure of Rabbit Muscle Glycogenin Complexed with UDP-glucose and Manganese'''<br />
 
-
==Overview==
+
==Crystal Structure of Rabbit Muscle Glycogenin Complexed with UDP-glucose and Manganese==
-
Glycogen is an important storage reserve of glucose present in many, organisms, from bacteria to humans. Its biosynthesis is initiated by a, specialized protein, glycogenin, which has the unusual property of, transferring glucose from UDP-glucose to form an oligosaccharide, covalently attached to itself at Tyr194. Glycogen synthase and the, branching enzyme complete the synthesis of the polysaccharide. The, structure of glycogenin was solved in two different crystal forms., Tetragonal crystals contained a pentamer of dimers in the asymmetric unit, arranged in an improper non-crystallographic 10-fold relationship, and, orthorhombic crystals contained a monomer in the asymmetric unit that is, arranged about a 2-fold crystallographic axis to form a dimer. The, structure was first solved to 3.4 A using the tetragonal crystal form and, a three-wavelength Se-Met multi-wavelength anomalous diffraction (MAD), experiment. Subsequently, an apo-enzyme structure and a complex between, glycogenin and UDP-glucose/Mn2+ were solved by molecular replacement to, 1.9 A using the orthorhombic crystal form. Glycogenin contains a conserved, DxD motif and an N-terminal beta-alpha-beta Rossmann-like fold that are, common to the nucleotide-binding domains of most glycosyltransferases., Although sequence identity amongst glycosyltransferases is minimal, the, overall folds are similar. In all of these enzymes, the DxD motif is, essential for coordination of the catalytic divalent cation, most commonly, Mn2+. We propose a mechanism in which the Mn2+ that associates with the, UDP-glucose molecule functions as a Lewis acid to stabilize the leaving, group UDP and to facilitate the transfer of the glucose moiety to an, intermediate nucleophilic acceptor in the enzyme active site, most likely, Asp162. Following transient transfer to Asp162, the glucose moiety is then, delivered to the final acceptor, either directly to Tyr194 or to glucose, residues already attached to Tyr194. The positioning of the bound, UDP-glucose far from Tyr194 in the glycogenin structure raises questions, as to the mechanism for the attachment of the first glucose residues., Possibly the initial glucosylation is via inter-dimeric catalysis with an, intra-molecular mechanism employed later in oligosaccharide synthesis.
+
<StructureSection load='1ll2' size='340' side='right'caption='[[1ll2]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1ll2]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LL2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LL2 FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UPG:URIDINE-5-DIPHOSPHATE-GLUCOSE'>UPG</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ll2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ll2 OCA], [https://pdbe.org/1ll2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ll2 RCSB], [https://www.ebi.ac.uk/pdbsum/1ll2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ll2 ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/GLYG_RABIT GLYG_RABIT] Self-glucosylates, via an inter-subunit mechanism, to form an oligosaccharide primer that serves as substrate for glycogen synthase.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ll/1ll2_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ll2 ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1LL2 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oryctolagus_cuniculus Oryctolagus cuniculus] with MN and UPG as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glycogenin_glucosyltransferase Glycogenin glucosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.1.186 2.4.1.186] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1LL2 OCA].
+
*[[Glycogenin|Glycogenin]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin., Gibbons BJ, Roach PJ, Hurley TD, J Mol Biol. 2002 May 31;319(2):463-77. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12051921 12051921]
+
[[Category: Large Structures]]
-
[[Category: Glycogenin glucosyltransferase]]
+
[[Category: Oryctolagus cuniculus]]
[[Category: Oryctolagus cuniculus]]
-
[[Category: Single protein]]
+
[[Category: Gibbons BJ]]
-
[[Category: Gibbons, B.J.]]
+
[[Category: Hurley TD]]
-
[[Category: Hurley, T.D.]]
+
[[Category: Roach PJ]]
-
[[Category: Roach, P.J.]]
+
-
[[Category: MN]]
+
-
[[Category: UPG]]
+
-
[[Category: beta-alpha-beta rossman-like nucleotide binding fold]]
+
-
[[Category: dxd motif]]
+
-
[[Category: non-proline cis peptide bond]]
+
-
[[Category: protein-substrate complex]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 20:38:34 2007''
+

Current revision

Crystal Structure of Rabbit Muscle Glycogenin Complexed with UDP-glucose and Manganese

PDB ID 1ll2

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ll2"
Personal tools