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| | ==Crystal structure of the N-glycan-deficient variant N448A of isopullulanase complexed with isopanose== | | ==Crystal structure of the N-glycan-deficient variant N448A of isopullulanase complexed with isopanose== |
| - | <StructureSection load='3wwg' size='340' side='right' caption='[[3wwg]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3wwg' size='340' side='right'caption='[[3wwg]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3wwg]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WWG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WWG FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3wwg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WWG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WWG FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=MAL:MALTOSE'>MAL</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wmr|1wmr]], [[1x0c|1x0c]], [[2z8g|2z8g]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=PRD_900001:alpha-maltose'>PRD_900001</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ipuA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5061 A. niger])</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=3wwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wwg OCA], [https://pdbe.org/3wwg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wwg RCSB], [https://www.ebi.ac.uk/pdbsum/3wwg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wwg ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isopullulanase Isopullulanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.57 3.2.1.57] </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=3wwg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wwg OCA], [http://pdbe.org/3wwg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wwg RCSB], [http://www.ebi.ac.uk/pdbsum/3wwg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wwg ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/IPUA_ASPNG IPUA_ASPNG]] Hydrolyzes pullulan, a linear polymer which is composed of maltotriose units with alpha-1,6 glucosidic linkages, to produce isopanose (Glca1-4Glca1-6Glc). | + | [https://www.uniprot.org/uniprot/IPUA_ASPNG IPUA_ASPNG] Hydrolyzes pullulan, a linear polymer which is composed of maltotriose units with alpha-1,6 glucosidic linkages, to produce isopanose (Glca1-4Glca1-6Glc). |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: A. niger]] | + | [[Category: Aspergillus niger]] |
| - | [[Category: Isopullulanase]] | + | [[Category: Large Structures]] |
| - | [[Category: Miyazaki, T]] | + | [[Category: Miyazaki T]] |
| - | [[Category: Nishikawa, A]] | + | [[Category: Nishikawa A]] |
| - | [[Category: Tonozuka, T]] | + | [[Category: Tonozuka T]] |
| - | [[Category: Yashiro, H]] | + | [[Category: Yashiro H]] |
| - | [[Category: Beta-helix]]
| + | |
| - | [[Category: Glycoside hydrolase family 49]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| Structural highlights
Function
IPUA_ASPNG Hydrolyzes pullulan, a linear polymer which is composed of maltotriose units with alpha-1,6 glucosidic linkages, to produce isopanose (Glca1-4Glca1-6Glc).
Publication Abstract from PubMed
N-glycosylation has been shown to be important for the stability of some glycoproteins. Isopullulanase (IPU), a polysaccharide-hydrolyzing enzyme, is a highly N-glycosylated protein, and IPU deglycosylation results in a decrease in thermostability. To investigate the function of N-glycan in IPU, we focused on an N-glycosylated residue located in the vicinity of the active site, Asn448. The thermostabilities of three IPU variants, Y440A, N448A and S450A, were 0.5-8.4 degrees C lower than the wild-type enzyme. The crystal structure of endoglycosidase H (Endo H)-treated N448A variant was determined. There are four IPU molecules, Mol-A, B, C and D, in the asymmetric unit. The conformation of a loop composed of amino acid residues 435-455 in Mol-C was identical to wild-type IPU, whereas the conformations of this loop in Mol-A, Mol-B and Mol-D were different from each other. These results suggest that the Asn448 side chain is primarily important for the stability of IPU. Our results indicate that mutation of only N-glycosylated Asn residue may lead to incorrect conclusion for the evaluation of the function of N-glycan. Usually, the structures of N-glycosylation sites form an extended configuration in IPU; however, the Asn448 site had an atypical structure that lacked this configuration.
The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase.,Miyazaki T, Yashiro H, Nishikawa A, Tonozuka T J Biochem. 2015 Apr;157(4):225-34. doi: 10.1093/jb/mvu065. Epub 2014 Oct 29. PMID:25359784[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Miyazaki T, Yashiro H, Nishikawa A, Tonozuka T. The side chain of a glycosylated asparagine residue is important for the stability of isopullulanase. J Biochem. 2015 Apr;157(4):225-34. doi: 10.1093/jb/mvu065. Epub 2014 Oct 29. PMID:25359784 doi:http://dx.doi.org/10.1093/jb/mvu065
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