3u3h - Revision history

OCA at 10:16, 1 March 2024

OCA — Fri, 01 Mar 2024 10:16:48 GMT

←Older revision		Revision as of 10:16, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3u3h]] 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=3U3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U3H FirstGlance]. <br>		<table><tr><td colspan='2'>[[3u3h]] 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=3U3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U3H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</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]] 0.97Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.5 5.3.1.5] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</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=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [https://pdbe.org/3u3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [https://www.ebi.ac.uk/pdbsum/3u3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3h 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=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [https://pdbe.org/3u3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [https://www.ebi.ac.uk/pdbsum/3u3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://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;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and D-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D<sub>2</sub>O was monitored by <sup>1</sup>H NMR spectroscopy and <i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 0.034 M<sup>-1</sup> s<sup>-1</sup> was determined for this isomerization at pD 7.0. This is similar to <i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 0.017 M<sup>-1</sup> s<sup>-1</sup> for the TIM-catalyzed carbon deprotonation reaction of DGA in D<sub>2</sub>O at pD 7.0 [Amyes, T. L.; O'Donoghue, A. C. and Richard J. P. (2001) <i>J. Am. Chem. Soc. 123</i>, 11325-11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 490 M<sup>-1</sup> s<sup>-1</sup>) than for the TIM-catalyzed isomerization of DGAP (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 9.6 x 10<sup>6</sup> M<sup>-1</sup> s<sup>-1</sup>) is due to: (i) The larger barrier to conversion of cyclic D-xylose to the reactive linear sugar (5.4 kcal/mol) than for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol). (ii) The smaller intrinsic binding energy [Jencks, W. P. (1975) <i>Adv. Enzymol. Relat. Areas Mol. Biol. 43</i>, 219-410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) than of the phosphodianion group of DGAP (ca. 12 kcal/mol). The XI catalyzed isomerization of DGA in D<sub>2</sub>O at pD 7.0 gives a 90% yield of [1-<sup>1</sup>H]-DHA and a 10% yield of [1-<sup>2</sup>H]-DHA, the product of isomerization with deuterium incorporation from solvent D<sub>2</sub>O. By comparison, the transfer of <sup>3</sup>H from labeled hexose substrate to solvent is observed only once in every 10<sup>9</sup> turnovers for the XI-catalyzed isomerization of [2-<sup>3</sup>H]-glucose in H<sub>2</sub>O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994), <i>Biochemistry 33</i>, 1481-1487]. We propose that truncation of the terminal ethylene glycol fragment of D-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high resolution (0.97 A) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI-sugar complexes.	+
-		+
-	Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde.,Toteva MM, Silvaggi NR, Allen KN, Richard JP Biochemistry. 2011 Oct 13. PMID:21995300<ref>PMID:21995300</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3u3h" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
-	*[[D-xylose isomerase\|D-xylose isomerase]]	+	*[[D-xylose isomerase 3D structures\|D-xylose isomerase 3D structures]]
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
-	~~[[Category: Xylose isomerase]]~~	+	[[Category: Allen KN]]
-	[[Category: Allen~~, K N~~]]	+	[[Category: Richard JP]]
-	[[Category: Richard~~, J P~~]]	+	[[Category: Silvaggi NR]]
-	[[Category: Silvaggi~~, N R~~]]	+	[[Category: Toteva MM]]
-	[[Category: Toteva~~, M M]]~~	+
-	~~[[Category: Aldose-ketose isomerase]]~~	+
-	~~[[Category: Enzyme promiscuity]]~~	+
-	~~[[Category: Glyceraldehyde]]~~	+
-	~~[[Category: Hydride shift]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 05:56, 13 July 2022

OCA — Wed, 13 Jul 2022 05:56:06 GMT

←Older revision		Revision as of 05:56, 13 July 2022
Line 1:		Line 1:

	==X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde==		==X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde==
-	<StructureSection load='3u3h' size='340' side='right' caption='[[3u3h]], [[Resolution\|resolution]] 0.97Å' scene=''>	+	<StructureSection load='3u3h' size='340' side='right'caption='[[3u3h]], [[Resolution\|resolution]] 0.97Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3u3h]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3U3H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3u3h]] 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=3U3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3U3H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Xylose_isomerase Xylose isomerase], with EC number [https://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=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [~~http~~://pdbe.org/3u3h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3u3h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3h 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=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [https://pdbe.org/3u3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [https://www.ebi.ac.uk/pdbsum/3u3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3h 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 26:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA at 11:51, 4 August 2016

OCA — Thu, 04 Aug 2016 11:51:09 GMT

←Older revision		Revision as of 11:51, 4 August 2016
Line 1:		Line 1:
		+
	==X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde==		==X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde==
	<StructureSection load='3u3h' size='340' side='right' caption='[[3u3h]], [[Resolution\|resolution]] 0.97Å' scene=''>		<StructureSection load='3u3h' size='340' side='right' caption='[[3u3h]], [[Resolution\|resolution]] 0.97Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</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='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=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [http://www.ebi.ac.uk/pdbsum/3u3h PDBsum]</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=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [http://pdbe.org/3u3h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [http://www.ebi.ac.uk/pdbsum/3u3h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3u3h ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3u3h" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 14:09, 24 December 2014

OCA — Wed, 24 Dec 2014 14:09:21 GMT

←Older revision		Revision as of 14:09, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3u3h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3H FirstGlance]. <br>		<table><tr><td colspan='2'>[[3u3h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3H FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene></td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [http://www.ebi.ac.uk/pdbsum/3u3h PDBsum]</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=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [http://www.ebi.ac.uk/pdbsum/3u3h PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://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 13:		Line 15:
	Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde.,Toteva MM, Silvaggi NR, Allen KN, Richard JP Biochemistry. 2011 Oct 13. PMID:21995300<ref>PMID:21995300</ref>		Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde.,Toteva MM, Silvaggi NR, Allen KN, Richard JP Biochemistry. 2011 Oct 13. PMID:21995300<ref>PMID:21995300</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>

Line 24:		Line 26:
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
-	[[Category: Allen, K N.]]	+	[[Category: Allen, K N]]
-	[[Category: Richard, J P.]]	+	[[Category: Richard, J P]]
-	[[Category: Silvaggi, N R.]]	+	[[Category: Silvaggi, N R]]
-	[[Category: Toteva, M M.]]	+	[[Category: Toteva, M M]]
	[[Category: Aldose-ketose isomerase]]		[[Category: Aldose-ketose isomerase]]
	[[Category: Enzyme promiscuity]]		[[Category: Enzyme promiscuity]]

OCA at 06:39, 5 June 2014

OCA — Thu, 05 Jun 2014 06:39:44 GMT

←Older revision		Revision as of 06:39, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3u3h.~~png~~\|~~left\|200px~~]]	+	==X-Ray Crystallographic Analysis of D-Xylose Isomerase-Catalyzed Isomerization of (R)-Glyceraldehyde==
		+	<StructureSection load='3u3h' size='340' side='right' caption='[[3u3h]], [[Resolution\|resolution]] 0.97Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3u3h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3U3H FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=03W:(2R)-PROPANE-1,1,2,3-TETROL'>03W</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene><br>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3u3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3u3h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3u3h RCSB], [http://www.ebi.ac.uk/pdbsum/3u3h PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and D-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D<sub>2</sub>O was monitored by <sup>1</sup>H NMR spectroscopy and <i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 0.034 M<sup>-1</sup> s<sup>-1</sup> was determined for this isomerization at pD 7.0. This is similar to <i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 0.017 M<sup>-1</sup> s<sup>-1</sup> for the TIM-catalyzed carbon deprotonation reaction of DGA in D<sub>2</sub>O at pD 7.0 [Amyes, T. L.; O'Donoghue, A. C. and Richard J. P. (2001) <i>J. Am. Chem. Soc. 123</i>, 11325-11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 490 M<sup>-1</sup> s<sup>-1</sup>) than for the TIM-catalyzed isomerization of DGAP (<i>k</i><sub>cat</sub>/<i>K</i><sub>m</sub> = 9.6 x 10<sup>6</sup> M<sup>-1</sup> s<sup>-1</sup>) is due to: (i) The larger barrier to conversion of cyclic D-xylose to the reactive linear sugar (5.4 kcal/mol) than for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol). (ii) The smaller intrinsic binding energy [Jencks, W. P. (1975) <i>Adv. Enzymol. Relat. Areas Mol. Biol. 43</i>, 219-410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) than of the phosphodianion group of DGAP (ca. 12 kcal/mol). The XI catalyzed isomerization of DGA in D<sub>2</sub>O at pD 7.0 gives a 90% yield of [1-<sup>1</sup>H]-DHA and a 10% yield of [1-<sup>2</sup>H]-DHA, the product of isomerization with deuterium incorporation from solvent D<sub>2</sub>O. By comparison, the transfer of <sup>3</sup>H from labeled hexose substrate to solvent is observed only once in every 10<sup>9</sup> turnovers for the XI-catalyzed isomerization of [2-<sup>3</sup>H]-glucose in H<sub>2</sub>O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994), <i>Biochemistry 33</i>, 1481-1487]. We propose that truncation of the terminal ethylene glycol fragment of D-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high resolution (0.97 A) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI-sugar complexes.

-	<!--	+	Binding Energy and Catalysis by D-Xylose Isomerase: Kinetic, Product and X-Ray Crystallographic Analysis of Enzyme-Catalyzed Isomerization of (R)-Glyceraldehyde.,Toteva MM, Silvaggi NR, Allen KN, Richard JP Biochemistry. 2011 Oct 13. PMID:21995300<ref>PMID:21995300</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3u3h", creates the "Structure Box" on the page.~~	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet)~~	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded~~),	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3u3h\| PDB=3u3h \| SCENE= }}~~	+

-	~~===X-Ray Crystallographic Analysis~~ of ~~D-Xylose Isomerase-Catalyzed Isomerization~~ of ~~(R)-Glyceraldehyde===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	~~<!--~~	+	*[[D-xylose isomerase\|D-xylose isomerase]]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21995300}}, adds the Publication Abstract to the page~~	+	== References ==
-	~~(as it appears on PubMed at http://www.pubmed.gov), where 21995300 is the PubMed ID number.~~	+	<references/>
-	~~-->~~	+	__TOC__
-	~~{{ABSTRACT_PUBMED_21995300}}~~	+	</StructureSection>
-		+
-	==~~About this Structure~~==	+
-	[[~~3u3h~~]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_rubiginosus Streptomyces rubiginosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3U3H OCA].	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021995300<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA: Protected "3u3h" [edit=sysop:move=sysop]

OCA — Sun, 30 Oct 2011 09:21:00 GMT

Protected "3u3h" [edit=sysop:move=sysop]

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Revision as of 09:21, 30 October 2011