2x2j: Difference between revisions

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[[Image:2x2j.png|left|200px]]


{{STRUCTURE_2x2j| PDB=2x2j | SCENE= }}
==Crystal structure of the Gracilariopsis lemaneiformis alpha- 1,4-glucan lyase with deoxynojirimycin==
<StructureSection load='2x2j' size='340' side='right'caption='[[2x2j]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2x2j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gracilariopsis_lemaneiformis Gracilariopsis lemaneiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X2J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X2J 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]] 2.35&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NOJ:1-DEOXYNOJIRIMYCIN'>NOJ</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=2x2j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x2j OCA], [https://pdbe.org/2x2j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x2j RCSB], [https://www.ebi.ac.uk/pdbsum/2x2j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x2j ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9STC1_GRALE Q9STC1_GRALE]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
alpha-1,4-Glucan lyase (EC 4.2.2.13) from the red seaweed Gracilariopsis lemaneiformis cleaves alpha-1,4-glucosidic linkages in glycogen, starch and malto-oligosaccharides, yielding the keto-monosaccharide 1,5-anhydro-D-fructose. The enzyme belongs to glycoside hydrolase family 31 (GH31), but degrades starch via an elimination reaction instead of hydrolysis. The crystal structure shows that the enzyme, like GH31 hydrolases, contains a (beta/alpha)8-barrel catalytic domain with B and B' subdomains, an N-terminal domain N, and the C-terminal domains C and D. The N-terminal domain N of the lyase was found to bind a trisaccharide. Complexes of the enzyme with acarbose and 1-dexoynojirimycin, and two different covalent glycosyl-enzyme intermediates obtained with fluorinated sugar analogues show that, like GH31 hydrolases, the aspartic acid residues D553 and D665 are the catalytic nucleophile and acid, respectively. However, as a unique feature, the catalytic nucleophile is in a position to act also as a base that abstracts a proton from the C2 carbon atom of the covalently bound subsite -1 glucosyl residue, thus explaining the enzyme's unique lyase activity. One Glu to Val mutation in the active site of the homologous alpha-glucosidase from Sulfolobus solfataricus resulted in a shift from hydrolytic to lyase activity, demonstrating that a subtle amino acid difference can promote lyase activity in a GH31 hydrolase.


===CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4-GLUCAN LYASE WITH DEOXYNOJIRIMYCIN===
Crystal structure of alpha-1,4-glucan lyase, a unique glycoside hydrolase family member with a novel catalytic mechanism.,Rozeboom HJ, Yu S, Madrid S, Kalk KH, Zhang R, Dijkstra BW J Biol Chem. 2013 Jul 31. PMID:23902768<ref>PMID:23902768</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
[[2x2j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Gracilariopsis_lemaneiformis Gracilariopsis lemaneiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2X2J OCA].
<div class="pdbe-citations 2x2j" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Gracilariopsis lemaneiformis]]
[[Category: Gracilariopsis lemaneiformis]]
[[Category: Dijkstra, B W.]]
[[Category: Large Structures]]
[[Category: Kalk, K H.]]
[[Category: Dijkstra BW]]
[[Category: Madrid, S.]]
[[Category: Kalk KH]]
[[Category: Rozeboom, H J.]]
[[Category: Madrid S]]
[[Category: Yu, S.]]
[[Category: Rozeboom HJ]]
[[Category: Anhydrofructose pathway]]
[[Category: Yu S]]
[[Category: Glycoside hydrolase family 31]]
[[Category: Lyase]]
[[Category: Starch binding domain]]
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