1xym - Revision history

OCA at 08:53, 14 February 2024

OCA — Wed, 14 Feb 2024 08:53:58 GMT

←Older revision		Revision as of 08:53, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1xym' size='340' side='right'caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xym' size='340' side='right'caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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]] 1.8Å</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=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [https://pdbe.org/1xym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [https://www.ebi.ac.uk/pdbsum/1xym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xym 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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [https://pdbe.org/1xym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [https://www.ebi.ac.uk/pdbsum/1xym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL]] Involved in D-xylose catabolism.	+	[https://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL] Involved in D-xylose catabolism.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xym ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xym ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The distinct roles of the two magnesium ions essential to the activity of D-xylose isomerase from Streptomyces olivochromogenes were examined. The enzyme-magnesium complex was isolated, and the stoichiometry of cation binding determined by neutron activation analysis to be 2 mol of magnesium per mole of enzyme. A plot of Mg2+ added versus Mg2+ bound to enzyme is consistent with apparent KD values of < or = 0.5-1.0 mM for one Mg2+ and < or = 2-5 mM for the second. A site-directed mutant of D-xylose isomerase was designed to remove the tighter, tetracoordinated magnesium binding site (site 1, Mg-1); Glu180 was replaced with Lys180. The stoichiometry of metal binding to this mutant, E180K, is 1 mol of magnesium per mole of enzyme. Ring-opening assays with 1-thioglucose (H2S released upon ring opening) show E180K catalyzes the opening of the sugar ring at 20% the rate of the wild-type, but E180K does not catalyze isomerization of glucose to fructose. Thus, the magnesium bound to Glu180 is essential for isomerization but not essential for ring opening. The X-ray crystallographic structures of E180K in the absence of magnesium and in the presence and absence of 250 mM glucose were obtained to 1.8-A resolution and refined to R factors of 17.7% and 19.7%, respectively. The wild-type and both E180K structures show no significant structural differences, except the epsilon-amino group of Lys180, which occupies the position usually occupied by the Mg-1.(ABSTRACT TRUNCATED AT 250 WORDS)
-
-	Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid.,Allen KN, Lavie A, Glasfeld A, Tanada TN, Gerrity DP, Carlson SC, Farber GK, Petsko GA, Ringe D Biochemistry. 1994 Feb 15;33(6):1488-94. PMID:7906142<ref>PMID:7906142</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1xym" 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: ~~Xylose isomerase~~]]	+	[[Category: Streptomyces olivochromogenes]]
-	[[Category: Allen~~, K N~~]]	+	[[Category: Allen KN]]
-	[[Category: Lavie, A]]	+	[[Category: Lavie A]]
-	[[Category: Petsko~~, G A~~]]	+	[[Category: Petsko GA]]
-	[[Category: Ringe, D]]	+	[[Category: Ringe D]]

OCA at 10:37, 13 April 2022

OCA — Wed, 13 Apr 2022 10:37:01 GMT

←Older revision		Revision as of 10:37, 13 April 2022
Line 3:		Line 3:
	<StructureSection load='1xym' size='340' side='right'caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xym' size='340' side='right'caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1XYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XYM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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~~://proteopedia.org/fgij/fg.htm?mol=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [~~http~~://pdbe.org/1xym PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1xym PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1xym 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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [https://pdbe.org/1xym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [https://www.ebi.ac.uk/pdbsum/1xym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL]] Involved in D-xylose catabolism.	+	[[https://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL]] Involved in D-xylose catabolism.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:13, 8 July 2020

OCA — Wed, 08 Jul 2020 14:13:56 GMT

←Older revision		Revision as of 14:13, 8 July 2020
Line 3:		Line 3:
	<StructureSection load='1xym' size='340' side='right'caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xym' size='340' side='right'caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1XYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1XYM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://pdbe.org/1xym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xym ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://pdbe.org/1xym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 11:32, 4 December 2019

OCA — Wed, 04 Dec 2019 11:32:06 GMT

←Older revision		Revision as of 11:32, 4 December 2019
Line 1:		Line 1:

	==THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID==		==THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID==
-	<StructureSection load='1xym' size='340' side='right' caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='1xym' size='340' side='right'caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYM FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xy/1xym_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xy/1xym_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1xym" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1xym" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[D-xylose isomerase\|D-xylose isomerase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Allen, K N]]		[[Category: Allen, K N]]

OCA at 07:02, 29 November 2017

OCA — Wed, 29 Nov 2017 07:02:05 GMT

←Older revision		Revision as of 07:02, 29 November 2017
Line 1:		Line 1:
		+
	==THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID==		==THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID==
	<StructureSection load='1xym' size='340' side='right' caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xym' size='340' side='right' caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://pdbe.org/1xym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym 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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://pdbe.org/1xym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1xym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1xym" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1xym" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[D-xylose isomerase\|D-xylose isomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:20, 8 February 2016

OCA — Mon, 08 Feb 2016 20:20:13 GMT

←Older revision		Revision as of 20:20, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1xym ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:03, 10 September 2015

OCA — Thu, 10 Sep 2015 15:03:19 GMT

←Older revision		Revision as of 15:03, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1xym' size='340' side='right' caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='1xym' size='340' side='right' caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Streptomyces_olivochromogenes Streptomyces olivochromogenes~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"actinomyces_olivochromogenus"_(sic)_waksman_1923 "actinomyces olivochromogenus" (sic) waksman 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym 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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://pdbe.org/1xym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 1xym" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Streptomyces olivochromogenes]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Allen, K N]]		[[Category: Allen, K N]]

OCA at 01:54, 25 December 2014

OCA — Thu, 25 Dec 2014 01:54:20 GMT

←Older revision		Revision as of 01:54, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYM FirstGlance]. <br>		<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym 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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/XYLA_STROL XYLA_STROL]] Involved in D-xylose catabolism.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	[[Category: Streptomyces olivochromogenes]]		[[Category: Streptomyces olivochromogenes]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
-	[[Category: Allen, K N.]]	+	[[Category: Allen, K N]]
-	[[Category: Lavie, A.]]	+	[[Category: Lavie, A]]
-	[[Category: Petsko, G A.]]	+	[[Category: Petsko, G A]]
-	[[Category: Ringe, D.]]	+	[[Category: Ringe, D]]

OCA at 21:29, 29 September 2014

OCA — Mon, 29 Sep 2014 21:29:53 GMT

←Older revision		Revision as of 21:29, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1xym.~~png\|left~~\|200px]]	+	==THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID==
		+	<StructureSection load='1xym' size='340' side='right' caption='[[1xym]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1xym]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1XYM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLO:D-GLUCOSE+IN+LINEAR+FORM'>GLO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</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=1xym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1xym RCSB], [http://www.ebi.ac.uk/pdbsum/1xym PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xy/1xym_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The distinct roles of the two magnesium ions essential to the activity of D-xylose isomerase from Streptomyces olivochromogenes were examined. The enzyme-magnesium complex was isolated, and the stoichiometry of cation binding determined by neutron activation analysis to be 2 mol of magnesium per mole of enzyme. A plot of Mg2+ added versus Mg2+ bound to enzyme is consistent with apparent KD values of < or = 0.5-1.0 mM for one Mg2+ and < or = 2-5 mM for the second. A site-directed mutant of D-xylose isomerase was designed to remove the tighter, tetracoordinated magnesium binding site (site 1, Mg-1); Glu180 was replaced with Lys180. The stoichiometry of metal binding to this mutant, E180K, is 1 mol of magnesium per mole of enzyme. Ring-opening assays with 1-thioglucose (H2S released upon ring opening) show E180K catalyzes the opening of the sugar ring at 20% the rate of the wild-type, but E180K does not catalyze isomerization of glucose to fructose. Thus, the magnesium bound to Glu180 is essential for isomerization but not essential for ring opening. The X-ray crystallographic structures of E180K in the absence of magnesium and in the presence and absence of 250 mM glucose were obtained to 1.8-A resolution and refined to R factors of 17.7% and 19.7%, respectively. The wild-type and both E180K structures show no significant structural differences, except the epsilon-amino group of Lys180, which occupies the position usually occupied by the Mg-1.(ABSTRACT TRUNCATED AT 250 WORDS)

-	~~{{STRUCTURE_1xym\| PDB=1xym \| SCENE= }}~~	+	Role of the divalent metal ion in sugar binding, ring opening, and isomerization by D-xylose isomerase: replacement of a catalytic metal by an amino acid.,Allen KN, Lavie A, Glasfeld A, Tanada TN, Gerrity DP, Carlson SC, Farber GK, Petsko GA, Ringe D Biochemistry. 1994 Feb 15;33(6):1488-94. PMID:7906142<ref>PMID:7906142</ref>

-	~~===THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING~~, ~~RING OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL BY AN AMINO-ACID===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7906142}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1xym]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Streptomyces_olivochromogenes Streptomyces olivochromogenes]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1XYM OCA].~~	+

	==See Also==		==See Also==
	*[[D-xylose isomerase\|D-xylose isomerase]]		*[[D-xylose isomerase\|D-xylose isomerase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:007906142<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Streptomyces olivochromogenes]]		[[Category: Streptomyces olivochromogenes]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA: Protected "1xym" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:46:51 GMT

Protected "1xym" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:46, 5 January 2013