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== | ==CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride== | ||
[[4amx]] is a 4 chain structure with sequence from [ | <StructureSection load='4amx' size='340' side='right'caption='[[4amx]], [[Resolution|resolution]] 2.10Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4amx]] 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=4AMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4AMX 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]] 2.1Å</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=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4amx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4amx OCA], [https://pdbe.org/4amx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4amx RCSB], [https://www.ebi.ac.uk/pdbsum/4amx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4amx 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 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 4amx" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Gracilariopsis lemaneiformis]] | [[Category: Gracilariopsis lemaneiformis]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Dijkstra BW]] | ||
[[Category: | [[Category: Kalk KH]] | ||
[[Category: | [[Category: Madrid S]] | ||
[[Category: Rozeboom HJ]] | |||
[[Category: | [[Category: Yu S]] | ||
[[Category: | |||
Latest revision as of 14:30, 20 December 2023
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
FunctionPublication 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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