3ww4 - Revision history

OCA at 19:22, 29 May 2024

OCA — Wed, 29 May 2024 19:22:42 GMT

←Older revision		Revision as of 19:22, 29 May 2024
Line 1:		Line 1:

	==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==		==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==
-	<StructureSection load='3ww4' size='340' side='right'caption='[[3ww4]]' scene=''>	+	<StructureSection load='3ww4' size='340' side='right'caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellulomonas_parahominis Cellulomonas parahominis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>
-	</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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [https://pdbe.org/3ww4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww4 ProSAT]</span></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]] 1.95Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [https://pdbe.org/3ww4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww4 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/L0N3Y0_9CELL L0N3Y0_9CELL]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	L-Ribose isomerase from Cellulomonas parahominis MB426 (CpL-RI) can catalyze the isomerization between L-ribose and L-ribulose, which are non-abundant in nature and called rare sugars. CpL-RI has a broad substrate specificity and can catalyze the isomerization between D-lyxose and D-xylulose, D-talose and D-tagatose, L-allose and L-psicose, L-gulose and L-sorbose, and D-mannose and D-fructose. To elucidate the molecular basis underlying the substrate recognition mechanism of CpL-RI, the crystal structures of CpL-RI alone and in complexes with L-ribose, L-allose, and L-psicose were determined. The structure of CpL-RI was very similar to that of L-ribose isomerase from Acinetobacter sp. strain DL-28, previously determined by us. CpL-RI had a cupin-type beta-barrel structure, and the catalytic site was detected between two large beta-sheets with a bound metal ion. The bound substrates coordinated to the metal ion, and Glu113 and Glu204 were shown to act as acid/base catalysts in the catalytic reaction via a cis-enediol intermediate. Glu211 and Arg243 were found to be responsible for the recognition of substrates with various configurations at 4- and 5-positions of sugar. CpL-RI formed a homo-tetramer in crystals, and the catalytic site independently consisted of residues within a subunit, suggesting that the catalytic site acted independently. Crystal structure and site-direct mutagenesis analyses showed that the tetramer structure is essential for the enzyme activity and that each subunit of CpL-RI could be structurally stabilized by intermolecular contacts with other subunits. The results of growth complementation assays suggest that CpL-RI is involved in a novel metabolic pathway using L-ribose as a carbon source.
		+
		+	Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway.,Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S Appl Microbiol Biotechnol. 2015 Feb 8. PMID:25661811<ref>PMID:25661811</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3ww4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cellulomonas parahominis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kamitori S]]		[[Category: Kamitori S]]

OCA at 10:37, 31 August 2022

OCA — Wed, 31 Aug 2022 10:37:20 GMT

←Older revision		Revision as of 10:37, 31 August 2022
Line 1:		Line 1:

	==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==		==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==
-	<StructureSection load='3ww4' size='340' side='right'caption='[[3ww4]]~~, [[Resolution\|resolution]] 1.95Å~~' scene=''>	+	<StructureSection load='3ww4' size='340' side='right'caption='[[3ww4]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3ww4]] is a 2 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>	+	</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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [https://pdbe.org/3ww4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww4 ProSAT]</span></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</div></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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [https://pdbe.org/3ww4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww4 ProSAT]</span></td></tr>	+
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	L-Ribose isomerase from Cellulomonas parahominis MB426 (CpL-RI) can catalyze the isomerization between L-ribose and L-ribulose, which are non-abundant in nature and called rare sugars. CpL-RI has a broad substrate specificity and can catalyze the isomerization between D-lyxose and D-xylulose, D-talose and D-tagatose, L-allose and L-psicose, L-gulose and L-sorbose, and D-mannose and D-fructose. To elucidate the molecular basis underlying the substrate recognition mechanism of CpL-RI, the crystal structures of CpL-RI alone and in complexes with L-ribose, L-allose, and L-psicose were determined. The structure of CpL-RI was very similar to that of L-ribose isomerase from Acinetobacter sp. strain DL-28, previously determined by us. CpL-RI had a cupin-type beta-barrel structure, and the catalytic site was detected between two large beta-sheets with a bound metal ion. The bound substrates coordinated to the metal ion, and Glu113 and Glu204 were shown to act as acid/base catalysts in the catalytic reaction via a cis-enediol intermediate. Glu211 and Arg243 were found to be responsible for the recognition of substrates with various configurations at 4- and 5-positions of sugar. CpL-RI formed a homo-tetramer in crystals, and the catalytic site independently consisted of residues within a subunit, suggesting that the catalytic site acted independently. Crystal structure and site-direct mutagenesis analyses showed that the tetramer structure is essential for the enzyme activity and that each subunit of CpL-RI could be structurally stabilized by intermolecular contacts with other subunits. The results of growth complementation assays suggest that CpL-RI is involved in a novel metabolic pathway using L-ribose as a carbon source.
-
-	Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway.,Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S Appl Microbiol Biotechnol. 2015 Feb 8. PMID:25661811<ref>PMID:25661811</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3ww4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kamitori, S]]	+	[[Category: Kamitori S]]
-	[[Category: Takata, G]]	+	[[Category: Takata G]]
-	[[Category: Terami, Y]]	+	[[Category: Terami Y]]
-	[[Category: Yoshida, H]]	+	[[Category: Yoshida H]]
-	~~[[Category: Cupin-type beta-barrel]]~~	+
-	~~[[Category: Isomerase~~]]	+

OCA at 04:59, 25 August 2022

OCA — Thu, 25 Aug 2022 04:59:53 GMT

←Older revision		Revision as of 04:59, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='3ww4' size='340' side='right'caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3ww4' size='340' side='right'caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure ~~with sequence from [https://en.wikipedia.org/wiki/'cellulomonas_parahominis' 'cellulomonas parahominis']~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</div></td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cellulomonas parahominis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]

OCA at 05:33, 10 August 2022

OCA — Wed, 10 Aug 2022 05:33:36 GMT

←Older revision		Revision as of 05:33, 10 August 2022
Line 1:		Line 1:

	==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==		==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==
-	<StructureSection load='3ww4' size='340' side='right' caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3ww4' size='340' side='right'caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/'cellulomonas_parahominis' 'cellulomonas parahominis']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/'cellulomonas_parahominis' 'cellulomonas parahominis']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</div></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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [~~http~~://pdbe.org/3ww4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ww4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww4 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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [https://pdbe.org/3ww4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [https://www.ebi.ac.uk/pdbsum/3ww4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Cellulomonas parahominis]]		[[Category: Cellulomonas parahominis]]
		+	[[Category: Large Structures]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]
	[[Category: Takata, G]]		[[Category: Takata, G]]

OCA at 09:38, 21 February 2019

OCA — Thu, 21 Feb 2019 09:38:57 GMT

←Older revision		Revision as of 09:38, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='3ww4' size='340' side='right' caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3ww4' size='340' side='right' caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'cellulomonas_parahominis' 'cellulomonas parahominis']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cellulomonas parahominis]]
	[[Category: Kamitori, S]]		[[Category: Kamitori, S]]
	[[Category: Takata, G]]		[[Category: Takata, G]]

OCA at 18:46, 1 February 2017

OCA — Wed, 01 Feb 2017 18:46:59 GMT

←Older revision		Revision as of 18:46, 1 February 2017
Line 1:		Line 1:
		+
	==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==		==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==
	<StructureSection load='3ww4' size='340' side='right' caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3ww4' size='340' side='right' caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww4 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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [http://pdbe.org/3ww4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ww4 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 3ww4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:31, 30 April 2015

OCA — Thu, 30 Apr 2015 11:31:59 GMT

←Older revision		Revision as of 11:31, 30 April 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose==
		+	<StructureSection load='3ww4' size='340' side='right' caption='[[3ww4]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ww4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WW4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WW4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3BU:L-ALLOSE'>3BU</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=WOO:BETA-L-ALLOPYRANOSE'>WOO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ww1\|3ww1]], [[3ww2\|3ww2]], [[3ww3\|3ww3]]</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=3ww4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ww4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ww4 RCSB], [http://www.ebi.ac.uk/pdbsum/3ww4 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	L-Ribose isomerase from Cellulomonas parahominis MB426 (CpL-RI) can catalyze the isomerization between L-ribose and L-ribulose, which are non-abundant in nature and called rare sugars. CpL-RI has a broad substrate specificity and can catalyze the isomerization between D-lyxose and D-xylulose, D-talose and D-tagatose, L-allose and L-psicose, L-gulose and L-sorbose, and D-mannose and D-fructose. To elucidate the molecular basis underlying the substrate recognition mechanism of CpL-RI, the crystal structures of CpL-RI alone and in complexes with L-ribose, L-allose, and L-psicose were determined. The structure of CpL-RI was very similar to that of L-ribose isomerase from Acinetobacter sp. strain DL-28, previously determined by us. CpL-RI had a cupin-type beta-barrel structure, and the catalytic site was detected between two large beta-sheets with a bound metal ion. The bound substrates coordinated to the metal ion, and Glu113 and Glu204 were shown to act as acid/base catalysts in the catalytic reaction via a cis-enediol intermediate. Glu211 and Arg243 were found to be responsible for the recognition of substrates with various configurations at 4- and 5-positions of sugar. CpL-RI formed a homo-tetramer in crystals, and the catalytic site independently consisted of residues within a subunit, suggesting that the catalytic site acted independently. Crystal structure and site-direct mutagenesis analyses showed that the tetramer structure is essential for the enzyme activity and that each subunit of CpL-RI could be structurally stabilized by intermolecular contacts with other subunits. The results of growth complementation assays suggest that CpL-RI is involved in a novel metabolic pathway using L-ribose as a carbon source.

-	~~The entry 3ww4 is ON HOLD until Paper Publication~~	+	Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway.,Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S Appl Microbiol Biotechnol. 2015 Feb 8. PMID:25661811<ref>PMID:25661811</ref>

-	~~Authors: Terami~~, Y.~~, Yoshida, H~~.~~, Takata, G~~., Kamitori, S.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose~~	+	== References ==
-	[[Category: ~~Unreleased Structures~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kamitori, S]]
		+	[[Category: Takata, G]]
	[[Category: Terami, Y]]		[[Category: Terami, Y]]
	[[Category: Yoshida, H]]		[[Category: Yoshida, H]]
-	[[Category: ~~Takata, G~~]]	+	[[Category: Cupin-type beta-barrel]]
-	[[Category: ~~Kamitori, S~~]]	+	[[Category: Isomerase]]

OCA at 13:02, 24 December 2014

OCA — Wed, 24 Dec 2014 13:02:00 GMT

←Older revision		Revision as of 13:02, 24 December 2014
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	Description: X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose		Description: X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose
		+	[[Category: Unreleased Structures]]
		+	[[Category: Terami, Y]]
		+	[[Category: Yoshida, H]]
		+	[[Category: Takata, G]]
		+	[[Category: Kamitori, S]]

OCA at 06:46, 30 July 2014

OCA — Wed, 30 Jul 2014 06:46:37 GMT

←Older revision		Revision as of 06:46, 30 July 2014
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ww4 is ON HOLD	+	The entry 3ww4 is ON HOLD until Paper Publication

	Authors: Terami, Y., Yoshida, H., Takata, G., Kamitori, S.		Authors: Terami, Y., Yoshida, H., Takata, G., Kamitori, S.

	Description: X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose		Description: X-ray structures of Cellulomonas parahominis L-ribose isomerase with L-allose

OCA: Protected "3ww4" [edit=sysop:move=sysop]

OCA — Wed, 18 Jun 2014 05:56:59 GMT

Protected "3ww4" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:56, 18 June 2014