4amw: Difference between revisions
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== | ==CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-idosyl- fluoride== | ||
[[4amw]] 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=4AMW OCA]. | <StructureSection load='4amw' size='340' side='right' caption='[[4amw]], [[Resolution|resolution]] 1.90Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4amw]] 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=4AMW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4AMW FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5DI:2-OXO-1,2,DIDEOXY-5F-D-IDOPYRANOSE'>5DI</scene>, <scene name='pdbligand=B9D:(2R,3R,4R,5S,6R)-6-FLUORANYL-6-(HYDROXYMETHYL)OXANE-2,3,4,5-TETROL'>B9D</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4amx|4amx]]</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4amw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amw OCA], [http://pdbe.org/4amw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4amw RCSB], [http://www.ebi.ac.uk/pdbsum/4amw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4amw ProSAT]</span></td></tr> | |||
</table> | |||
<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 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> | |||
<ref | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4amw" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Gracilariopsis lemaneiformis]] | [[Category: Gracilariopsis lemaneiformis]] | ||
[[Category: Dijkstra, B W | [[Category: Dijkstra, B W]] | ||
[[Category: Kalk, K H | [[Category: Kalk, K H]] | ||
[[Category: Madrid, S | [[Category: Madrid, S]] | ||
[[Category: Rozeboom, H J | [[Category: Rozeboom, H J]] | ||
[[Category: Yu, S | [[Category: Yu, S]] | ||
[[Category: Anhydrofructose pathway]] | [[Category: Anhydrofructose pathway]] | ||
[[Category: Glycoside hydrolase family 31]] | [[Category: Glycoside hydrolase family 31]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Secondary carbohydrate binding site]] | [[Category: Secondary carbohydrate binding site]] | ||
