5x32 - Revision history

OCA at 07:53, 22 November 2023

OCA — Wed, 22 Nov 2023 07:53:33 GMT

←Older revision		Revision as of 07:53, 22 November 2023
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	==Crystal structure of D-mannose isomerase==		==Crystal structure of D-mannose isomerase==
-	<StructureSection load='5x32' size='340' side='right' caption='[[5x32]], [[Resolution\|resolution]] 2.59Å' scene=''>	+	<StructureSection load='5x32' size='340' side='right'caption='[[5x32]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x32]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Marm1 Marm1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X32 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X32 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x32]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Marinomonas_mediterranea_MMB-1 Marinomonas mediterranea MMB-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X32 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.586Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Marme_2490 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=717774 MARM1])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=5x32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x32 OCA], [~~http~~://pdbe.org/5x32 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x32 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x32 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x32 ProSAT]</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=5x32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x32 OCA], [https://pdbe.org/5x32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x32 RCSB], [https://www.ebi.ac.uk/pdbsum/5x32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x32 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MANI_MARM1 MANI_MARM1] Catalyzes the reversible isomerization of D-mannose to D-fructose. Can also isomerize D-lyxose, with lower efficiency. In longer reaction with a higher concentration of enzyme, it can isomerize 4-OH D-mannose derivatives (D-talose and 4-O-monosaccharyl-D-mannose). Cannot use D-glucose.<ref>PMID:29107017</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Marm1~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kato, K~~]]	+	[[Category: Marinomonas mediterranea MMB-1]]
-	[[Category: ~~Saburi, W~~]]	+	[[Category: Kato K]]
-	[[Category: ~~Yao, M~~]]	+	[[Category: Saburi W]]
-	[[Category: ~~Isomerase~~]]	+	[[Category: Yao M]]

OCA at 07:11, 28 February 2018

OCA — Wed, 28 Feb 2018 07:11:41 GMT

←Older revision		Revision as of 07:11, 28 February 2018
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	<StructureSection load='5x32' size='340' side='right' caption='[[5x32]], [[Resolution\|resolution]] 2.59Å' scene=''>		<StructureSection load='5x32' size='340' side='right' caption='[[5x32]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x32]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X32 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X32 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x32]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Marm1 Marm1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X32 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X32 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Marme_2490 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=717774 MARM1])</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=5x32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x32 OCA], [http://pdbe.org/5x32 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x32 RCSB], [http://www.ebi.ac.uk/pdbsum/5x32 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x32 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=5x32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x32 OCA], [http://pdbe.org/5x32 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x32 RCSB], [http://www.ebi.ac.uk/pdbsum/5x32 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x32 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	d-Mannose isomerase (MI) reversibly isomerizes d-mannose to d-fructose, and is attractive for producing d-mannose from inexpensive d-fructose. It belongs to the N-acylglucosamine 2-epimerase (AGE) superfamily along with AGE, cellobiose 2-epimerase (CE), and aldose-ketose isomerase (AKI). In this study, Marinomonas mediterranea Marme_2490, showing low sequence identity with any known enzymes, was found to isomerize d-mannose as its primary substrate. Marme_2490 also isomerized d-lyxose and 4-OH d-mannose derivatives (d-talose and 4-O-monosaccharyl-d-mannose). Its activity for d-lyxose is known in other d-mannose isomerizing enzymes, such as MI and AKI, but we identified, for the first time, its activity for 4-OH d-mannose derivatives. Marme_2490 did not isomerize d-glucose, as known MIs do not, while AKI isomerizes both d-mannose and d-glucose. Thus, Marme_2490 was concluded to be an MI. The initial and equilibrium reaction products were analyzed by NMR to illuminate mechanistic information regarding the Marme_2490 reaction. The analysis of the initial reaction product revealed that beta-d-mannose was formed. In the analysis of the equilibrated reaction products in D2O, signals of 2-H of d-mannose and 1-H of d-fructose were clearly detected. This indicates that these protons are not substituted with deuterium from D2O and Marme_2490 catalyzes the intramolecular proton transfer between 1-C and 2-C. The crystal structure of Marme_2490 in a ligand-free form was determined and found that Marme_2490 is formed by an (alpha/alpha)6-barrel, which is commonly observed in AGE superfamily enzymes. Despite diverse reaction specificities, the orientations of residues involved in catalysis and substrate binding by Marme_2490 were similar to those in both AKI (Salmonella enterica AKI) and epimerase (Rhodothermus marinus CE). The Marme_2490 structure suggested that the alpha7-->alpha8 and alpha11-->alpha12 loops of the catalytic domain participated in the formation of an open substrate-binding site to provide sufficient space to bind 4-OH d-mannose derivatives.
		+
		+	Biochemical and structural characterization of Marinomonas mediterranead-mannose isomerase Marme_2490 phylogenetically distant from known enzymes.,Saburi W, Jaito N, Kato K, Tanaka Y, Yao M, Mori H Biochimie. 2018 Jan;144:63-73. doi: 10.1016/j.biochi.2017.10.016. Epub 2017 Oct, 26. PMID:29107017<ref>PMID:29107017</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5x32" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Marm1]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Saburi, W]]		[[Category: Saburi, W]]
	[[Category: Yao, M]]		[[Category: Yao, M]]
	[[Category: Isomerase]]		[[Category: Isomerase]]

OCA at 06:15, 7 February 2018

OCA — Wed, 07 Feb 2018 06:15:06 GMT

←Older revision		Revision as of 06:15, 7 February 2018
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-	'''Unreleased structure'''

-	~~The entry~~ 5x32 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of D-mannose isomerase==
-		+	<StructureSection load='5x32' size='340' side='right' caption='[[5x32]], [[Resolution\|resolution]] 2.59Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5x32]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X32 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X32 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5x32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x32 OCA], [http://pdbe.org/5x32 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x32 RCSB], [http://www.ebi.ac.uk/pdbsum/5x32 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x32 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kato, K]]
		+	[[Category: Saburi, W]]
		+	[[Category: Yao, M]]
		+	[[Category: Isomerase]]

OCA: Protected "5x32" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:41:11 GMT

Protected "5x32" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:41, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x32 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Thu, 09 Mar 2017 15:41:10 GMT

New page: '''Unreleased structure''' The entry 5x32 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5x32 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]