2gl9: Difference between revisions
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New page: left|200px<br /><applet load="2gl9" size="450" color="white" frame="true" align="right" spinBox="true" caption="2gl9, resolution 2.00Å" /> '''Crystal Structure of... |
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== | ==Crystal Structure of Glycosylasparaginase-Substrate Complex== | ||
Glycosylasparaginase (GA) plays an important role in asparagine-linked | <StructureSection load='2gl9' size='340' side='right'caption='[[2gl9]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2gl9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Elizabethkingia_meningoseptica Elizabethkingia meningoseptica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GL9 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]] 2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASN:ASPARAGINE'>ASN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=2gl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gl9 OCA], [https://pdbe.org/2gl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gl9 RCSB], [https://www.ebi.ac.uk/pdbsum/2gl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gl9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/ASPG_ELIMR ASPG_ELIMR] Cleaves the GlcNAc-Asn bond which joins oligosaccharides to the peptide of asparagine-linked glycoproteins. Requires that the glycosylated asparagine moiety is not substituted on its N-(R1) and C- (R2) terminus. | |||
== 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/gl/2gl9_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2gl9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Glycosylasparaginase (GA) plays an important role in asparagine-linked glycoprotein degradation. A deficiency in the activity of human GA leads to a lysosomal storage disease named aspartylglycosaminuria. GA belongs to a superfamily of N-terminal nucleophile hydrolases that autoproteolytically generate their mature enzymes from inactive single chain protein precursors. The side-chain of the newly exposed N-terminal residue then acts as a nucleophile during substrate hydrolysis. By taking advantage of mutant enzyme of Flavobacterium meningosepticum GA with reduced enzymatic activity, we have obtained a crystallographic snapshot of a productive complex with its substrate (NAcGlc-Asn), at 2.0 A resolution. This complex structure provided us an excellent model for the Michaelis complex to examine the specific contacts critical for substrate binding and catalysis. Substrate binding induces a conformational change near the active site of GA. To initiate catalysis, the side-chain of the N-terminal Thr152 is polarized by the free alpha-amino group on the same residue, mediated by the side-chain hydroxyl group of Thr170. Cleavage of the amide bond is then accomplished by a nucleophilic attack at the carbonyl carbon of the amide linkage in the substrate, leading to the formation of an acyl-enzyme intermediate through a negatively charged tetrahedral transition state. | |||
Crystallographic snapshot of a productive glycosylasparaginase-substrate complex.,Wang Y, Guo HC J Mol Biol. 2007 Feb 9;366(1):82-92. Epub 2006 Sep 26. PMID:17157318<ref>PMID:17157318</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2gl9" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Asparaginase 3D structures|Asparaginase 3D structures]] | |||
*[[Glycosylasparaginase|Glycosylasparaginase]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Elizabethkingia meningoseptica]] | [[Category: Elizabethkingia meningoseptica]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: Guo HC]] | |||
[[Category: Guo | [[Category: Wang Y]] | ||
[[Category: Wang | |||
