3kcl - Revision history

OCA at 10:16, 21 February 2024

OCA — Wed, 21 Feb 2024 10:16:22 GMT

←Older revision		Revision as of 10:16, 21 February 2024
Line 1:		Line 1:

	==Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)==		==Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)==
-	<StructureSection load='3kcl' size='340' side='right' caption='[[3kcl]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3kcl' size='340' side='right'caption='[[3kcl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kcl]] 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=3KCL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kcl]] 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=3KCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KCL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Hybrid , Neutron Diffraction , X-ray diffraction, [[Resolution\|Resolution]] 2Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kbj\|3kbj]]~~, ~~[[3kbm\|3kbm]]~~, ~~[[3kbn\|3kbn]]~~, [[~~3kbs~~\|~~3kbs]], [[3kbv\|3kbv]], [[3kbw\|3kbw]], [[3kcj\|3kcj]], [[3kco\|3kco~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kcl OCA], [https://pdbe.org/3kcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kcl RCSB], [https://www.ebi.ac.uk/pdbsum/3kcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kcl ProSAT]</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=3kcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kcl OCA], [~~http~~://pdbe.org/3kcl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kcl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kcl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kcl 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.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kc/3kcl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kc/3kcl_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 22:		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=3kcl 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=3kcl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

-	~~Metal ion roles and the movement of hydrogen during reaction catalyzed by~~ D-xylose isomerase~~: a joint x~~-ray and neutron diffraction study.,Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P Structure. 2010 Jun 9;18(6):688-99. PMID:20541506<ref>PMID:20541506</ref>	+	==See Also==
-		+	*[[D-xylose isomerase 3D structures\|D-xylose isomerase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3kcl" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__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: Kovalevsky~~, A Y~~]]	+	[[Category: Kovalevsky AY]]
-	[[Category: Langan, P]]	+	[[Category: Langan P]]
-	~~[[Category: Carbohydrate metabolism]]~~	+
-	~~[[Category: Deuterated glucose]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Pentose shunt]]~~	+
-	~~[[Category: Xylose metabolism~~]]	+

OCA at 08:31, 1 November 2017

OCA — Wed, 01 Nov 2017 08:31:10 GMT

←Older revision		Revision as of 08:31, 1 November 2017
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3kcl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3kcl" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[D-xylose isomerase\|D-xylose isomerase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:40, 5 August 2016

OCA — Fri, 05 Aug 2016 09:40:39 GMT

←Older revision		Revision as of 09:40, 5 August 2016
Line 1:		Line 1:
		+
	==Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)==		==Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)==
	<StructureSection load='3kcl' size='340' side='right' caption='[[3kcl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3kcl' size='340' side='right' caption='[[3kcl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kcl]] 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=3KCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kcl]] 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=3KCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KCL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kbj\|3kbj]], [[3kbm\|3kbm]], [[3kbn\|3kbn]], [[3kbs\|3kbs]], [[3kbv\|3kbv]], [[3kbw\|3kbw]], [[3kcj\|3kcj]], [[3kco\|3kco]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kbj\|3kbj]], [[3kbm\|3kbm]], [[3kbn\|3kbn]], [[3kbs\|3kbs]], [[3kbv\|3kbv]], [[3kbw\|3kbw]], [[3kcj\|3kcj]], [[3kco\|3kco]]</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 ~~Streptomyces~~ rubiginosus])</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='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=3kcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kcl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kcl RCSB], [http://www.ebi.ac.uk/pdbsum/3kcl 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=3kcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kcl OCA], [http://pdbe.org/3kcl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kcl RCSB], [http://www.ebi.ac.uk/pdbsum/3kcl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kcl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3kcl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3kcl" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 38:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Streptomyces~~ rubiginosus]]	+	[[Category: Actinomyces rubiginosus preobrazhenskaya et al. in gauze et al. 1957]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Kovalevsky, A Y]]		[[Category: Kovalevsky, A Y]]

OCA at 17:44, 25 December 2014

OCA — Thu, 25 Dec 2014 17:44:22 GMT

←Older revision		Revision as of 17:44, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3kcl]] 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=3KCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KCL FirstGlance]. <br>		<table><tr><td colspan='2'>[[3kcl]] 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=3KCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KCL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kbj\|3kbj]], [[3kbm\|3kbm]], [[3kbn\|3kbn]], [[3kbs\|3kbs]], [[3kbv\|3kbv]], [[3kbw\|3kbw]], [[3kcj\|3kcj]], [[3kco\|3kco]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kbj\|3kbj]], [[3kbm\|3kbm]], [[3kbn\|3kbn]], [[3kbs\|3kbs]], [[3kbv\|3kbv]], [[3kbw\|3kbw]], [[3kcj\|3kcj]], [[3kco\|3kco]]</td></tr>
-	<tr><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 Streptomyces rubiginosus])</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 Streptomyces rubiginosus])</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=3kcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kcl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kcl RCSB], [http://www.ebi.ac.uk/pdbsum/3kcl 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=3kcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kcl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kcl RCSB], [http://www.ebi.ac.uk/pdbsum/3kcl PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/XYLA_STRRU XYLA_STRRU]] Involved in D-xylose catabolism.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 27:
	Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.,Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P Structure. 2010 Jun 9;18(6):688-99. PMID:20541506<ref>PMID:20541506</ref>		Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.,Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P Structure. 2010 Jun 9;18(6):688-99. PMID:20541506<ref>PMID:20541506</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>
		+
		+	==See Also==
		+	*[[D-xylose isomerase\|D-xylose isomerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 38:
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
-	[[Category: Kovalevsky, A Y.]]	+	[[Category: Kovalevsky, A Y]]
-	[[Category: Langan, P.]]	+	[[Category: Langan, P]]
	[[Category: Carbohydrate metabolism]]		[[Category: Carbohydrate metabolism]]
	[[Category: Deuterated glucose]]		[[Category: Deuterated glucose]]
Line 40:		Line 45:
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Pentose shunt]]		[[Category: Pentose shunt]]
-	[[Category: Xylose isomerase]]
	[[Category: Xylose metabolism]]		[[Category: Xylose metabolism]]

OCA at 09:49, 21 May 2014

OCA — Wed, 21 May 2014 09:49:12 GMT

←Older revision		Revision as of 09:49, 21 May 2014
Line 1:		Line 1:
-	[[~~Image:~~3kcl.~~png~~\|~~left~~\|200px]]	+	==Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)==
		+	<StructureSection load='3kcl' size='340' side='right' caption='[[3kcl]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3kcl]] 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=3KCL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KCL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=DOD:DEUTERATED+WATER'>DOD</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3kbj\|3kbj]], [[3kbm\|3kbm]], [[3kbn\|3kbn]], [[3kbs\|3kbs]], [[3kbv\|3kbv]], [[3kbw\|3kbw]], [[3kcj\|3kcj]], [[3kco\|3kco]]</td></tr>
		+	<tr><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 Streptomyces rubiginosus])</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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3kcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kcl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kcl RCSB], [http://www.ebi.ac.uk/pdbsum/3kcl 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/kc/3kcl_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 ==
		+	Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

-	<!--	+	Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.,Kovalevsky AY, Hanson L, Fisher SZ, Mustyakimov M, Mason SA, Forsyth VT, Blakeley MP, Keen DA, Wagner T, Carrell HL, Katz AK, Glusker JP, Langan P Structure. 2010 Jun 9;18(6):688-99. PMID:20541506<ref>PMID:20541506</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3kcl"~~, ~~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_3kcl\| PDB=3kcl \| SCENE= }}~~	+

-	~~===Room temperature neutron structure~~ of ~~D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in~~ the ~~ring form (refined jointly with X-ray structure 3KBM)===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20541506}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 20541506 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_20541506}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3kcl]] 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=3KCL OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:020541506<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

OCA at 04:58, 8 March 2012

OCA — Thu, 08 Mar 2012 04:58:18 GMT

←Older revision		Revision as of 04:58, 8 March 2012
Line 11:		Line 11:
	===Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)===		===Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20541506}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20541506 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20541506}}

	==About this Structure==		==About this Structure==
	[[3kcl]] 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=3KCL OCA].		[[3kcl]] 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=3KCL OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:020541506</ref><references group="xtra"/>
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]

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

OCA — Wed, 27 Jul 2011 05:15:08 GMT

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

←Older revision

Revision as of 05:15, 27 July 2011

OCA at 05:15, 27 July 2011

OCA — Wed, 27 Jul 2011 05:15:07 GMT

←Older revision		Revision as of 05:15, 27 July 2011
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3kcl.png\|left\|200px]]
-	[[Image:3kcl.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 14:		Line 13:

	==About this Structure==		==About this Structure==
-	~~3KCL~~ 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=3KCL OCA].	+	[[3kcl]] 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=3KCL OCA].
	[[Category: Streptomyces rubiginosus]]		[[Category: Streptomyces rubiginosus]]
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
Line 26:		Line 25:
	[[Category: Xylose isomerase]]		[[Category: Xylose isomerase]]
	[[Category: Xylose metabolism]]		[[Category: Xylose metabolism]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:38:52 2010''

OCA at 04:33, 16 June 2010

OCA — Wed, 16 Jun 2010 04:33:52 GMT

←Older revision		Revision as of 04:33, 16 June 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kcl.jpg\|left\|200px]]

-	The ~~entry 3kcl~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kcl", 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_3kcl\| PDB=3kcl \| SCENE= }}

-	~~Authors: Kovalevsky, A.Y., Langan, P.~~	+	===Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)===

-	Description: Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 14 09~~:19:15 2010''	+	==About this Structure==
		+	3KCL 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=3KCL OCA].
		+	[[Category: Streptomyces rubiginosus]]
		+	[[Category: Xylose isomerase]]
		+	[[Category: Kovalevsky, A Y.]]
		+	[[Category: Langan, P.]]
		+	[[Category: Carbohydrate metabolism]]
		+	[[Category: Deuterated glucose]]
		+	[[Category: Isomerase]]
		+	[[Category: Metal-binding]]
		+	[[Category: Pentose shunt]]
		+	[[Category: Xylose isomerase]]
		+	[[Category: Xylose metabolism]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:38:52 2010''

OCA at 06:19, 14 April 2010

OCA — Wed, 14 Apr 2010 06:19:16 GMT

←Older revision		Revision as of 06:19, 14 April 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3kcl is ON HOLD	+	The entry 3kcl is ON HOLD until Paper Publication

	Authors: Kovalevsky, A.Y., Langan, P.		Authors: Kovalevsky, A.Y., Langan, P.
Line 7:		Line 7:
	Description: Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)		Description: Room temperature neutron structure of D-Xylose Isomerase in complex with two Cd2+ cations and d12-D-alpha-glucose in the ring form (refined jointly with X-ray structure 3KBM)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Oct 28 13~~:00:~~39 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 14 09:19:15 2010''