5y4i - Revision history

OCA at 08:21, 22 November 2023

OCA — Wed, 22 Nov 2023 08:21:43 GMT

←Older revision		Revision as of 08:21, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of glucose isomerase in complex with glycerol in one metal binding mode==		==Crystal structure of glucose isomerase in complex with glycerol in one metal binding mode==
-	<StructureSection load='5y4i' size='340' side='right' caption='[[5y4i]], [[Resolution\|resolution]] 1.91Å' scene=''>	+	<StructureSection load='5y4i' size='340' side='right'caption='[[5y4i]], [[Resolution\|resolution]] 1.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y4i]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"actinomyces_rubiginosus"_preobrazhenskaya_et_al._in_gauze_et_al._1957 "actinomyces~~ rubiginosus~~" preobrazhenskaya et al. in gauze et al. 1957~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y4I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y4I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y4i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y4I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=ACT:ACETATE+ION'>ACT</scene~~>, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.91Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>xylA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1929~~ "~~Actinomyces rubiginosus~~" ~~Preobrazhenskaya et al. in Gauze et al. 1957])~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5]~~ </~~span~~></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=5y4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y4i OCA], [https://pdbe.org/5y4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y4i RCSB], [https://www.ebi.ac.uk/pdbsum/5y4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y4i ProSAT]</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=5y4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y4i OCA], [~~http~~://pdbe.org/5y4i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y4i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y4i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y4i ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU]] Involved in D-xylose catabolism.	+	[https://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU] Involved in D-xylose catabolism.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Actinomyces rubiginosus preobrazhenskaya et al. in gauze et al. 1957~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Xylose isomerase~~]]	+	[[Category: Streptomyces rubiginosus]]
-	[[Category: Bae~~, J E~~]]	+	[[Category: Bae JE]]
-	[[Category: Kim~~, I J~~]]	+	[[Category: Kim IJ]]
-	[[Category: Nam~~, K H]]~~	+	[[Category: Nam KH]]
-	~~[[Category: Glucose isomerase]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA: Protected "5y4i" [edit=sysop:move=sysop]

OCA — Wed, 01 Nov 2017 06:08:05 GMT

Protected "5y4i" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:08, 1 November 2017

OCA: New page: ==Crystal structure of glucose isomerase in complex with glycerol in one metal binding mode== == Structural highlights ==
<table><tr><td colspan='2'>[[5y4i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_rubiginosus"_preobrazhenskaya_et_al._in_gauze_et_al._1957 "actinomyces rubiginosus" preobrazhenskaya et al. in gauze et al. 1957]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y4I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y4I FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">xylA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1929 "Actinomyces rubiginosus" Preobrazhenskaya et al. in Gauze et al. 1957])</td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </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=5y4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y4i OCA], [http://pdbe.org/5y4i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y4i RCSB], [http://www.ebi.ac.uk/pdbsum/5y4i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y4i ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU]] Involved in D-xylose catabolism.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Glucose isomerase (GI) is an intramolecular oxidoreductase that interconverts aldoses and ketoses. These characteristics are widely used in the food, detergent, and pharmaceutical industries. In order to obtain an efficient GI, identification of novel GI genes and substrate binding/inhibition have been studied. Xylitol is a well-known inhibitor of GI. In Streptomyces rubiginosus, two crystal structures have been reported for GI in complex with xylitol inhibitor. However, a structural comparison showed that xylitol can have variable conformation at the substrate binding site, e.g., a nonspecific binding mode. In this study, we report the crystal structure of S. rubiginosus GI in a complex with xylitol and glycerol. Our crystal structure showed one metal binding mode in GI, which we presumed to represent the inactive form of the GI. The metal ion was found only at the M1 site, which was involved in substrate binding, and was not present at the M2 site, which was involved in catalytic function. The O2 and O4 atoms of xylitol molecules contributed to the stable octahedral coordination of the metal in M1. Although there was no metal at the M2 site, no large conformational change was observed for the conserved residues coordinating M2. Our structural analysis showed that the metal at the M2 site was not important when a xylitol inhibitor was bound to the M1 site in GI. Thus, these findings provided important information for elucidation or engineering of GI functions.

Crystal structure of glucose isomerase in complex with xylitol inhibitor in one metal binding mode.,Bae JE, Kim IJ, Nam KH Biochem Biophys Res Commun. 2017 Nov 4;493(1):666-670. doi:, 10.1016/j.bbrc.2017.08.134. Epub 2017 Sep 1. PMID:28865958<ref>PMID:28865958</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5y4i" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Actinomyces rubiginosus preobrazhenskaya et al. in gauze et al. 1957]]
[[Category: Xylose isomerase]]
[[Category: Bae, J E]]
[[Category: Kim, I J]]
[[Category: Nam, K H]]
[[Category: Glucose isomerase]]
[[Category: Isomerase]]