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==CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride== | ==CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride== | ||
<StructureSection load='4amx' size='340' side='right' caption='[[4amx]], [[Resolution|resolution]] 2.10Å' scene=''> | <StructureSection load='4amx' size='340' side='right'caption='[[4amx]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4amx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cordylecladia_lemanaeformis Cordylecladia lemanaeformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMX OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[4amx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Cordylecladia_lemanaeformis Cordylecladia lemanaeformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4AMX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=4AMX FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GF:5-FLUORO-BETA-D-GLUCOPYRANOSE'>5GF</scene>, <scene name='pdbligand=AFR:2-OXO-1,2,DIDEOXY-5F-D-GLUCOPYRANOSE'>AFR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GF:5-FLUORO-BETA-D-GLUCOPYRANOSE'>5GF</scene>, <scene name='pdbligand=AFR:2-OXO-1,2,DIDEOXY-5F-D-GLUCOPYRANOSE'>AFR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4amw|4amw]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4amw|4amw]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-(1->4)-alpha-D-glucan_lyase Exo-(1->4)-alpha-D-glucan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.13 4.2.2.13] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Exo-(1->4)-alpha-D-glucan_lyase Exo-(1->4)-alpha-D-glucan lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.13 4.2.2.13] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=4amx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amx OCA], [http://pdbe.org/4amx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4amx RCSB], [http://www.ebi.ac.uk/pdbsum/4amx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4amx ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Cordylecladia lemanaeformis]] | [[Category: Cordylecladia lemanaeformis]] | ||
[[Category: Large Structures]] | |||
[[Category: Dijkstra, B W]] | [[Category: Dijkstra, B W]] | ||
[[Category: Kalk, K H]] | [[Category: Kalk, K H]] | ||
Revision as of 11:13, 4 November 2020
CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluorideCRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride
Structural highlights
Publication Abstract from PubMedalpha-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 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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