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4ad5

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Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-deoxymannojirimycin and alpha-1,2-mannobiose

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 ==Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-deoxymannojirimycin and alpha-1,2-mannobiose==
-<StructureSection load='4ad5' size='340' side='right' caption='[[4ad5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='4ad5' size='340' side='right'caption='[[4ad5]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ad5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_sp._xb1a Bacteroides sp. xb1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AD5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ad5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_xylanisolvens_XB1A Bacteroides xylanisolvens XB1A]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AD5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AD5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMJ:1-DEOXYMANNOJIRIMYCIN'>DMJ</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ad0|4ad0]], [[4ad4|4ad4]], [[4acy|4acy]], [[4ad3|4ad3]], [[4ad1|4ad1]], [[4ad2|4ad2]], [[4acz|4acz]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMJ:1-DEOXYMANNOJIRIMYCIN'>DMJ</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PRD_900111:2alpha-alpha-mannobiose'>PRD_900111</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycoprotein_endo-alpha-1,2-mannosidase Glycoprotein endo-alpha-1,2-mannosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.130 3.2.1.130] </span></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=4ad5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ad5 OCA], [https://pdbe.org/4ad5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ad5 RCSB], [https://www.ebi.ac.uk/pdbsum/4ad5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ad5 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ad5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ad5 OCA], [http://pdbe.org/4ad5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ad5 RCSB], [http://www.ebi.ac.uk/pdbsum/4ad5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ad5 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/D6D1V7_9BACE D6D1V7_9BACE]
-N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-alpha-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-alpha-mannosidase. Structures solved at resolutions 1.7-2.1 A reveal a (beta/alpha)(8) barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc(1/3)Man(9)GlcNAc(2) yields Glc(1/3)-Man. Using the bespoke substrate alpha-Glc-1,3-alpha-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-alpha-mannosidase inhibitor alpha-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, alpha-Glc-1,3-isofagomine, and with the reducing-end product alpha-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.
-Structural and mechanistic insight into N-glycan processing by endo-alpha-mannosidase.,Thompson AJ, Williams RJ, Hakki Z, Alonzi DS, Wennekes T, Gloster TM, Songsrirote K, Thomas-Oates JE, Wrodnigg TM, Spreitz J, Stutz AE, Butters TD, Williams SJ, Davies GJ Proc Natl Acad Sci U S A. 2012 Jan 4. PMID:22219371<ref>PMID:22219371</ref>
+==See Also==
+*[[Mannosidase 3D structures|Mannosidase 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4ad5" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacteroides sp. xb1a]]
+[[Category: Bacteroides xylanisolvens XB1A]]
-[[Category: Glycoprotein endo-alpha-1,2-mannosidase]]
+[[Category: Large Structures]]
-[[Category: Alonzi, D S]]
+[[Category: Alonzi DS]]
-[[Category: Butters, T D]]
+[[Category: Butters TD]]
-[[Category: Davies, G J]]
+[[Category: Davies GJ]]
-[[Category: Gloster, T M]]
+[[Category: Gloster TM]]
-[[Category: Hakki, Z]]
+[[Category: Hakki Z]]
-[[Category: Songsrirote, K]]
+[[Category: Songsrirote K]]
-[[Category: Spreitz, J]]
+[[Category: Spreitz J]]
-[[Category: Stuetz, A E]]
+[[Category: Stuetz AE]]
-[[Category: Thomas-Oates, J E]]
+[[Category: Thomas-Oates JE]]
-[[Category: Thompson, A J]]
+[[Category: Thompson AJ]]
-[[Category: Wennekes, T]]
+[[Category: Wennekes T]]
-[[Category: Williams, R J]]
+[[Category: Williams RJ]]
-[[Category: Williams, S J]]
+[[Category: Williams SJ]]
-[[Category: Wrodnigg, T M]]
+[[Category: Wrodnigg TM]]
-[[Category: Cazy]]
-[[Category: Endomannosidase]]
-[[Category: Enzyme-carbohydrate interaction]]
-[[Category: Gh99]]
-[[Category: Glycoside hydrolase]]
-[[Category: Hydrolase]]
-[[Category: Mannose glycosidase inhibition]]

4ad5

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Structure of the GH99 endo-alpha-mannosidase from Bacteroides xylanisolvens in complex with glucose-1,3-deoxymannojirimycin and alpha-1,2-mannobiose

Structural highlights

Function

See Also

Contents

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