1ogd - Revision history

OCA at 08:59, 9 May 2024

2024-05-09T08:59:57Z

←Older revision		Revision as of 08:59, 9 May 2024
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	</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=1ogd 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=1ogd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose function is unknown among the seven gene products of the l-fucose regulon. Here we report the crystal structures of Bacillus subtilis RbsD, which reveals a novel decameric toroidal assembly of the protein. Nuclear magnetic resonance and other studies on RbsD reveal that the intersubunit cleft of the protein binds specific forms of d-ribose, but it does not have an enzyme activity toward the sugar. Likewise, FucU binds l-fucose but lacks an enzyme activity toward this sugar. We conclude that RbsD and FucU are cytoplasmic sugar-binding proteins, a novel class of proteins whose functional role may lie in helping influx of the sugar substrates.
		+
		+	Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture.,Kim MS, Shin J, Lee W, Lee HS, Oh BH J Biol Chem. 2003 Jul 25;278(30):28173-80. Epub 2003 May 8. PMID:12738765<ref>PMID:12738765</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1ogd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribose-binding protein\|Ribose-binding protein]]		*[[Ribose-binding protein\|Ribose-binding protein]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 05:47, 17 April 2024

2024-04-17T05:47:14Z

←Older revision		Revision as of 05:47, 17 April 2024
Line 1:		Line 1:

	==The Structure of Bacillus subtilis RbsD complexed with D-ribose==		==The Structure of Bacillus subtilis RbsD complexed with D-ribose==
-	<StructureSection load='1ogd' size='340' side='right'caption='[[1ogd]]' scene=''>	+	<StructureSection load='1ogd' size='340' side='right'caption='[[1ogd]], [[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=1OGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OGD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ogd]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OGD 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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [https://pdbe.org/1ogd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [https://www.ebi.ac.uk/pdbsum/1ogd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ogd 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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [https://pdbe.org/1ogd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [https://www.ebi.ac.uk/pdbsum/1ogd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ogd ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RBSD_BACSU RBSD_BACSU] Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose (By similarity).[HAMAP-Rule:MF_01661]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Kim M-S]]		[[Category: Kim M-S]]
	[[Category: Oh B-H]]		[[Category: Oh B-H]]

OCA at 15:23, 3 March 2021

2021-03-03T15:23:26Z

←Older revision		Revision as of 15:23, 3 March 2021
Line 1:		Line 1:

	==The Structure of Bacillus subtilis RbsD complexed with D-ribose==		==The Structure of Bacillus subtilis RbsD complexed with D-ribose==
-	<StructureSection load='1ogd' size='340' side='right'caption='[[1ogd]]~~, [[Resolution\|resolution]] 1.95Å~~' scene=''>	+	<StructureSection load='1ogd' size='340' side='right'caption='[[1ogd]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[1ogd]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1OGD FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OGD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [https://pdbe.org/1ogd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [https://www.ebi.ac.uk/pdbsum/1ogd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ogd ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [~~http~~://pdbe.org/1ogd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ogd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ogd ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[http://www.uniprot.org/uniprot/RBSD_BACSU RBSD_BACSU]] Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose (By similarity).[HAMAP-Rule:MF_01661]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 16:
	</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=1ogd 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=1ogd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose function is unknown among the seven gene products of the l-fucose regulon. Here we report the crystal structures of Bacillus subtilis RbsD, which reveals a novel decameric toroidal assembly of the protein. Nuclear magnetic resonance and other studies on RbsD reveal that the intersubunit cleft of the protein binds specific forms of d-ribose, but it does not have an enzyme activity toward the sugar. Likewise, FucU binds l-fucose but lacks an enzyme activity toward this sugar. We conclude that RbsD and FucU are cytoplasmic sugar-binding proteins, a novel class of proteins whose functional role may lie in helping influx of the sugar substrates.
-
-	Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture.,Kim MS, Shin J, Lee W, Lee HS, Oh BH J Biol Chem. 2003 Jul 25;278(30):28173-80. Epub 2003 May 8. PMID:12738765<ref>PMID:12738765</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ogd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Ribose-binding protein\|Ribose-binding protein]]		*[[Ribose-binding protein\|Ribose-binding protein]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim, M S]]	+	[[Category: Kim M-S]]
-	[[Category: Oh, B H]]	+	[[Category: Oh B-H]]
-	~~[[Category: Ribose]]~~	+
-	~~[[Category: Sugar transport]]~~	+
-	~~[[Category: Transport~~]]	+

OCA at 07:05, 23 May 2019

2019-05-23T07:05:04Z

←Older revision		Revision as of 07:05, 23 May 2019
Line 1:		Line 1:

	==The Structure of Bacillus subtilis RbsD complexed with D-ribose==		==The Structure of Bacillus subtilis RbsD complexed with D-ribose==
-	<StructureSection load='1ogd' size='340' side='right' caption='[[1ogd]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='1ogd' size='340' side='right'caption='[[1ogd]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ogd]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OGD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ogd]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OGD FirstGlance]. <br>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1ogd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ogd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribose-binding protein\|Ribose-binding protein]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
		+	[[Category: Large Structures]]
	[[Category: Kim, M S]]		[[Category: Kim, M S]]
	[[Category: Oh, B H]]		[[Category: Oh, B H]]

OCA at 07:11, 7 February 2018

2018-02-07T07:11:50Z

←Older revision		Revision as of 07:11, 7 February 2018
Line 1:		Line 1:
-	==~~THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH~~ D-~~RIBOSE~~==	+
		+	==The Structure of Bacillus subtilis RbsD complexed with D-ribose==
	<StructureSection load='1ogd' size='340' side='right' caption='[[1ogd]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='1ogd' size='340' side='right' caption='[[1ogd]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [http://pdbe.org/1ogd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [http://www.ebi.ac.uk/pdbsum/1ogd 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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [http://pdbe.org/1ogd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [http://www.ebi.ac.uk/pdbsum/1ogd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ogd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/1ogd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/og/1ogd_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 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 1ogd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ogd" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Ribose-binding protein\|Ribose-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:55, 8 February 2016

2016-02-08T19:55:26Z

←Older revision		Revision as of 19:55, 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=1ogd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:52, 10 September 2015

2015-09-10T14:52:01Z

←Older revision		Revision as of 14:52, 10 September 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [http://www.ebi.ac.uk/pdbsum/1ogd 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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [http://pdbe.org/1ogd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [http://www.ebi.ac.uk/pdbsum/1ogd 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 1ogd" style="background-color:#fffaf0;"></div>

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

OCA at 01:47, 25 December 2014

2014-12-25T01:47:37Z

←Older revision		Revision as of 01:47, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ogd]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OGD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ogd]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OGD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [http://www.ebi.ac.uk/pdbsum/1ogd 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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [http://www.ebi.ac.uk/pdbsum/1ogd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RBSD_BACSU RBSD_BACSU]] Catalyzes the interconversion of beta-pyran and beta-furan forms of D-ribose (By similarity).[HAMAP-Rule:MF_01661]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
-	[[Category: Kim, M S.]]	+	[[Category: Kim, M S]]
-	[[Category: Oh, B H.]]	+	[[Category: Oh, B H]]
	[[Category: Ribose]]		[[Category: Ribose]]
	[[Category: Sugar transport]]		[[Category: Sugar transport]]
	[[Category: Transport]]		[[Category: Transport]]

OCA at 16:46, 28 September 2014

2014-09-28T16:46:17Z

←Older revision		Revision as of 16:46, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ogd.~~png~~\|~~left~~\|200px]]	+	==THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH D-RIBOSE==
		+	<StructureSection load='1ogd' size='340' side='right' caption='[[1ogd]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ogd]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OGD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=RIP:RIBOSE(PYRANOSE+FORM)'>RIP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ogc\|1ogc]], [[1oge\|1oge]], [[1ogf\|1ogf]]</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=1ogd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ogd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ogd RCSB], [http://www.ebi.ac.uk/pdbsum/1ogd 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/og/1ogd_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 ==
		+	RbsD is the only protein whose biochemical function is unknown among the six gene products of the rbs operon involved in the active transport of ribose. FucU, a paralogue of RbsD conserved from bacteria to human, is also the only protein whose function is unknown among the seven gene products of the l-fucose regulon. Here we report the crystal structures of Bacillus subtilis RbsD, which reveals a novel decameric toroidal assembly of the protein. Nuclear magnetic resonance and other studies on RbsD reveal that the intersubunit cleft of the protein binds specific forms of d-ribose, but it does not have an enzyme activity toward the sugar. Likewise, FucU binds l-fucose but lacks an enzyme activity toward this sugar. We conclude that RbsD and FucU are cytoplasmic sugar-binding proteins, a novel class of proteins whose functional role may lie in helping influx of the sugar substrates.

-	~~{{STRUCTURE_1ogd\| PDB=1ogd \| SCENE= }}~~	+	Crystal structures of RbsD leading to the identification of cytoplasmic sugar-binding proteins with a novel folding architecture.,Kim MS, Shin J, Lee W, Lee HS, Oh BH J Biol Chem. 2003 Jul 25;278(30):28173-80. Epub 2003 May 8. PMID:12738765<ref>PMID:12738765</ref>

-	~~===THE STRUCTURE OF BACILLUS SUBTILIS RBSD COMPLEXED WITH D-RIBOSE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12738765}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ogd]] is~~ a ~~5 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA].~~	+

	==See Also==		==See Also==
	*[[Ribose-binding protein\|Ribose-binding protein]]		*[[Ribose-binding protein\|Ribose-binding protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012738765<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Kim, M S.]]		[[Category: Kim, M S.]]

OCA at 11:18, 20 October 2012

2012-10-20T11:18:06Z

←Older revision		Revision as of 11:18, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ogd]] is a 5 chain structure ~~of [[Ribose-binding protein]]~~ with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA].	+	[[1ogd]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OGD OCA].

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