5zyc - Revision history

OCA at 09:10, 22 November 2023

OCA — Wed, 22 Nov 2023 09:10:18 GMT

←Older revision		Revision as of 09:10, 22 November 2023
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	==Crystal Structure of Glucose Isomerase Soaked with Mn2+==		==Crystal Structure of Glucose Isomerase Soaked with Mn2+==
-	<StructureSection load='5zyc' size='340' side='right' caption='[[5zyc]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5zyc' size='340' side='right'caption='[[5zyc]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zyc]] 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=5ZYC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZYC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zyc]] 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=5ZYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZYC 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=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.75Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5zyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyc OCA], [https://pdbe.org/5zyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zyc RCSB], [https://www.ebi.ac.uk/pdbsum/5zyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyc 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=5zyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyc OCA], [~~http~~://pdbe.org/5zyc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zyc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zyc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyc 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: Nam~~, K H]]~~	+	[[Category: Nam KH]]
-	~~[[Category: Glucose isomerase]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 20:23, 2 December 2018

OCA — Sun, 02 Dec 2018 20:23:33 GMT

←Older revision		Revision as of 20:23, 2 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zyc is ~~ON HOLD~~	+	==Crystal Structure of Glucose Isomerase Soaked with Mn2+==
		+	<StructureSection load='5zyc' size='340' side='right' caption='[[5zyc]], [[Resolution\|resolution]] 1.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zyc]] 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=5ZYC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZYC 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5zyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyc OCA], [http://pdbe.org/5zyc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zyc RCSB], [http://www.ebi.ac.uk/pdbsum/5zyc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyc 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) catalyzes the reversible enzymatic isomerization of d-glucose and d-xylose to d-fructose and d-xylulose, respectively. This is one of the most important enzymes in the production of high-fructose corn syrup (HFCS) and biofuel. We recently determined the crystal structure of GI from S. rubiginosus (SruGI) complexed with a xylitol inhibitor in one metal binding mode. Although we assessed inhibitor binding at the M1 site, the metal binding at the M2 site and the substrate recognition mechanism for SruGI remains the unclear. Here, we report the crystal structure of the two metal binding modes of SruGI and its complex with glucose. This study provides a snapshot of metal binding at the SruGI M2 site in the presence of Mn(2+), but not in the presence of Mg(2+). Metal binding at the M2 site elicits a configuration change at the M1 site. Glucose molecule can only bind to the M1 site in presence of Mn(2+) at the M2 site. Glucose and Mn(2+) at the M2 site were bridged by water molecules using a hydrogen bonding network. The metal binding geometry of the M2 site indicates a distorted octahedral coordination with an angle of 55-110 degrees , whereas the M1 site has a relatively stable octahedral coordination with an angle of 85-95 degrees . We suggest a two-step sequential process for SruGI substrate recognition, in Mn(2+) binding mode, at the M2 site. Our results provide a better understanding of the molecular role of the M2 site in GI substrate recognition.

-	~~Authors:~~ Nam, K.H.	+	Structural analysis of substrate recognition by glucose isomerase in Mn(2+) binding mode at M2 site in S. rubiginosus.,Bae JE, Hwang KY, Nam KH Biochem Biophys Res Commun. 2018 Sep 5;503(2):770-775. doi:, 10.1016/j.bbrc.2018.06.074. Epub 2018 Jun 18. PMID:29909012<ref>PMID:29909012</ref>

-	~~Description: Crystal Structure~~ of ~~Glucose Isomerase Soaked with Mn2+~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Nam, K.H]]	+	<div class="pdbe-citations 5zyc" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Actinomyces rubiginosus preobrazhenskaya et al. in gauze et al. 1957]]
		+	[[Category: Xylose isomerase]]
		+	[[Category: Nam, K H]]
		+	[[Category: Glucose isomerase]]
		+	[[Category: Isomerase]]

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

OCA — Wed, 30 May 2018 03:56:33 GMT

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

←Older revision

Revision as of 03:56, 30 May 2018

OCA: New page: '''Unreleased structure''' The entry 5zyc is ON HOLD Authors: Nam, K.H. Description: Crystal Structure of Glucose Isomerase Soaked with Mn2+ Category: Unreleased Structures [[Categ...

OCA — Wed, 30 May 2018 03:56:32 GMT

New page: '''Unreleased structure''' The entry 5zyc is ON HOLD Authors: Nam, K.H. Description: Crystal Structure of Glucose Isomerase Soaked with Mn2+ Category: Unreleased Structures [[Categ...

New page

'''Unreleased structure'''

The entry 5zyc is ON HOLD

Authors: Nam, K.H.

Description: Crystal Structure of Glucose Isomerase Soaked with Mn2+
[[Category: Unreleased Structures]]
[[Category: Nam, K.H]]