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2gl9

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[[Image:2gl9.gif|left|200px]]
 
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==Crystal Structure of Glycosylasparaginase-Substrate Complex==
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The line below this paragraph, containing "STRUCTURE_2gl9", creates the "Structure Box" on the page.
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<StructureSection load='2gl9' size='340' side='right'caption='[[2gl9]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<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>
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{{STRUCTURE_2gl9| PDB=2gl9 | SCENE= }}
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<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>
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</table>
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== Function ==
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[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gl/2gl9_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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'''Crystal Structure of Glycosylasparaginase-Substrate Complex'''
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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>
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==Overview==
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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.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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2GL9 is a [[Protein complex]] structure of sequences from [http://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].
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</div>
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<div class="pdbe-citations 2gl9" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17157318 17157318]
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*[[Asparaginase 3D structures|Asparaginase 3D structures]]
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*[[Glycosylasparaginase|Glycosylasparaginase]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Elizabethkingia meningoseptica]]
[[Category: Elizabethkingia meningoseptica]]
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[[Category: Protein complex]]
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[[Category: Large Structures]]
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[[Category: Guo, H C.]]
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[[Category: Guo HC]]
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[[Category: Wang, Y.]]
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[[Category: Wang Y]]
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[[Category: Catalytic mechanism]]
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[[Category: Crystal structure]]
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[[Category: Electron-pair transfer]]
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[[Category: Enzyme-acyl intermediate]]
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[[Category: Enzyme-substrate complex]]
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[[Category: Glycosylasparaginase]]
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[[Category: Ntn-hydrolase]]
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[[Category: Nucleophilic attack]]
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[[Category: Oxyanion hole]]
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[[Category: Proton-relay network]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 05:13:46 2008''
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Current revision

Crystal Structure of Glycosylasparaginase-Substrate Complex

PDB ID 2gl9

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