2x2i: Difference between revisions

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~~{{STRUCTURE_2x2i| PDB=2x2i | SCENE= }}~~

~~===Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase with acarbose===~~

~~{{ABSTRACT_PUBMED_23902768}}~~

==~~About this Structure~~==

==Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase with acarbose==

[[2x2i]] 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=2X2I OCA].

== Structural highlights ==

<table><tr><td colspan='2'>[[2x2i]] 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=2X2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X2I 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]] 2.6Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AC1:6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL'>AC1</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900022:beta-acarbose'>PRD_900022</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=2x2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x2i OCA], [https://pdbe.org/2x2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x2i RCSB], [https://www.ebi.ac.uk/pdbsum/2x2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x2i ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/Q9STC1_GRALE Q9STC1_GRALE]

== 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.

~~==Reference==~~

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®/PubMed®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

__TOC__

</StructureSection>

[[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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@@ Line 1: / Line 1: @@
-{{STRUCTURE_2x2i|  PDB=2x2i  |  SCENE=  }}
-===Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase with acarbose===
-{{ABSTRACT_PUBMED_23902768}}
-==About this Structure==
+==Crystal structure of the Gracilariopsis lemaneiformis alpha-1,4- glucan lyase with acarbose==
-[[2x2i]] 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=2X2I OCA].
+<StructureSection load='2x2i' size='340' side='right'caption='[[2x2i]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2x2i]] 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=2X2I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2X2I 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]] 2.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AC1:6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL'>AC1</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PRD_900022:beta-acarbose'>PRD_900022</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=2x2i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2x2i OCA], [https://pdbe.org/2x2i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2x2i RCSB], [https://www.ebi.ac.uk/pdbsum/2x2i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2x2i 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.
-==Reference==
+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 group="xtra">PMID:023902768</ref><references group="xtra"/><references/>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2x2i" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[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]]