2z8e - Revision history

OCA at 13:56, 13 March 2024

OCA — Wed, 13 Mar 2024 13:56:34 GMT

←Older revision		Revision as of 13:56, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2z8e' size='340' side='right'caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='2z8e' size='340' side='right'caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~As_1.2186 As 1.2186~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~"><~~scene name~~='~~pdbligand~~=~~MES~~:~~2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'~~>~~MES~~</~~scene~~>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene>, <scene name='pdbligand=~~GAL~~:~~BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</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]] 1.99Å</td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [~~http~~://pdbe.org/2z8e PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z8e PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8e 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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [https://pdbe.org/2z8e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [https://www.ebi.ac.uk/pdbsum/2z8e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8e ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A8W790_BIFLN A8W790_BIFLN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		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=2z8e 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=2z8e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Recently, a gene cluster involving a phosphorylase specific for lacto-N-biose I (LNB; Galbeta1-3GlcNAc) and galacto-N-biose (GNB; Galbeta1-3GalNAc) has been found in Bifidobacterium longum. We showed that the solute-binding protein of a putative ATP-binding cassette-type transporter encoded in the cluster crystallizes only in the presence of LNB or GNB, and therefore we named it GNB/LNB-binding protein (GL-BP). Isothermal titration calorimetry measurements revealed that GL-BP specifically binds LNB and GNB with K(d) values of 0.087 and 0.010 microm, respectively, and the binding process is enthalpy-driven. The crystal structures of GL-BP complexed with LNB, GNB, and lacto-N-tetraose (Galbeta1-3GlcNAcbeta1-3Galbeta1-4Glc) were determined. The interactions between GL-BP and the disaccharide ligands mainly occurred through water-mediated hydrogen bonds. In comparison with the LNB complex, one additional hydrogen bond was found in the GNB complex. These structural characteristics of ligand binding are in agreement with the thermodynamic properties. The overall structure of GL-BP was similar to that of maltose-binding protein; however, the mode of ligand binding and the thermodynamic properties of these proteins were significantly different.
-
-	Structural and thermodynamic analyses of solute-binding Protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I.,Suzuki R, Wada J, Katayama T, Fushinobu S, Wakagi T, Shoun H, Sugimoto H, Tanaka A, Kumagai H, Ashida H, Kitaoka M, Yamamoto K J Biol Chem. 2008 May 9;283(19):13165-73. Epub 2008 Mar 10. PMID:18332142<ref>PMID:18332142</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2z8e" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[ABC transporter 3D structures\|ABC transporter 3D structures]]		*[[ABC transporter 3D structures\|ABC transporter 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~As 1 2186~~]]	+	[[Category: Bifidobacterium longum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fushinobu, S]]	+	[[Category: Fushinobu S]]
-	[[Category: Katayama, T]]	+	[[Category: Katayama T]]
-	[[Category: Suzuki, R]]	+	[[Category: Suzuki R]]
-	[[Category: Wada, J]]	+	[[Category: Wada J]]
-	~~[[Category: Abc transporter]]~~	+
-	~~[[Category: Human milk oligosacchalide]]~~	+
-	~~[[Category: Mucin core-1]]~~	+
-	~~[[Category: Sugar binding protein~~]]	+

OCA at 11:59, 29 July 2020

OCA — Wed, 29 Jul 2020 11:59:44 GMT

←Older revision		Revision as of 11:59, 29 July 2020
Line 1:		Line 1:

	==The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose==		==The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose==
-	<StructureSection load='2z8e' size='340' side='right' caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>	+	<StructureSection load='2z8e' size='340' side='right'caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_1.2186 As 1.2186]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_1.2186 As 1.2186]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~GAL~~:~~BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~MES~~:~~2-(N-MORPHOLINO)-ETHANESULFONIC~~+~~ACID~~'>~~MES~~</scene>, <scene name='pdbligand=~~NGA~~:~~N-ACETYL~~-D-~~GALACTOSAMINE~~'>~~NGA~~</scene>, <scene name='pdbligand=ZN:~~ZINC+ION~~'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://pdbe.org/2z8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8e 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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://pdbe.org/2z8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8e ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 29:		Line 29:

	==See Also==		==See Also==
-	*[[ABC transporter\|ABC transporter]]	+	*[[ABC transporter 3D structures\|ABC transporter 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: As 1 2186]]		[[Category: As 1 2186]]
		+	[[Category: Large Structures]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
	[[Category: Katayama, T]]		[[Category: Katayama, T]]

OCA at 08:54, 17 October 2018

OCA — Wed, 17 Oct 2018 08:54:59 GMT

←Older revision		Revision as of 08:54, 17 October 2018
Line 1:		Line 1:
		+
	==The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose==		==The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose==
	<StructureSection load='2z8e' size='340' side='right' caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='2z8e' size='340' side='right' caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_1.2186 As 1.2186]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_1.2186 As 1.2186]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MES~~:2-(N-~~MORPHOLINO)-ETHANESULFONIC+ACID~~'>~~MES~~</scene>, <scene name='pdbligand=ZN:~~ZINC~~+~~ION~~'>ZN</scene>, <scene name='pdbligand=~~GAL~~:~~BETA~~-D-~~GALACTOSE~~'>~~GAL~~</scene>, <scene name='pdbligand=~~NGA~~:~~N-ACETYL-D-GALACTOSAMINE~~'>~~NGA~~</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://pdbe.org/2z8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e 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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://pdbe.org/2z8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8e ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z8/2z8e_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z8/2z8e_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>

OCA at 09:02, 8 February 2016

OCA — Mon, 08 Feb 2016 09:02:26 GMT

←Older revision		Revision as of 09:02, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2z8e' size='340' side='right' caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='2z8e' size='340' side='right' caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bifidobacterium_longum Bifidobacterium longum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/As_1.2186 As 1.2186]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e 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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://pdbe.org/2z8e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 15:
	<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=2z8e ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	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 2z8e" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bifidobacterium longum~~]]	+	[[Category: As 1 2186]]
	[[Category: Fushinobu, S]]		[[Category: Fushinobu, S]]
	[[Category: Katayama, T]]		[[Category: Katayama, T]]

OCA at 07:47, 20 January 2015

OCA — Tue, 20 Jan 2015 07:47:59 GMT

←Older revision		Revision as of 07:47, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e 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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Bifidobacterium longum]]		[[Category: Bifidobacterium longum]]
-	[[Category: Fushinobu, S.]]	+	[[Category: Fushinobu, S]]
-	[[Category: Katayama, T.]]	+	[[Category: Katayama, T]]
-	[[Category: Suzuki, R.]]	+	[[Category: Suzuki, R]]
-	[[Category: Wada, J.]]	+	[[Category: Wada, J]]
	[[Category: Abc transporter]]		[[Category: Abc transporter]]
	[[Category: Human milk oligosacchalide]]		[[Category: Human milk oligosacchalide]]
	[[Category: Mucin core-1]]		[[Category: Mucin core-1]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]

OCA at 06:23, 29 September 2014

OCA — Mon, 29 Sep 2014 06:23:14 GMT

←Older revision		Revision as of 06:23, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2z8e.~~png~~\|~~left~~\|200px]]	+	==The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose==
		+	<StructureSection load='2z8e' size='340' side='right' caption='[[2z8e]], [[Resolution\|resolution]] 1.99Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8E FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z8d\|2z8d]], [[2z8f\|2z8f]]</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=2z8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z8e RCSB], [http://www.ebi.ac.uk/pdbsum/2z8e 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/z8/2z8e_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 ==
		+	Recently, a gene cluster involving a phosphorylase specific for lacto-N-biose I (LNB; Galbeta1-3GlcNAc) and galacto-N-biose (GNB; Galbeta1-3GalNAc) has been found in Bifidobacterium longum. We showed that the solute-binding protein of a putative ATP-binding cassette-type transporter encoded in the cluster crystallizes only in the presence of LNB or GNB, and therefore we named it GNB/LNB-binding protein (GL-BP). Isothermal titration calorimetry measurements revealed that GL-BP specifically binds LNB and GNB with K(d) values of 0.087 and 0.010 microm, respectively, and the binding process is enthalpy-driven. The crystal structures of GL-BP complexed with LNB, GNB, and lacto-N-tetraose (Galbeta1-3GlcNAcbeta1-3Galbeta1-4Glc) were determined. The interactions between GL-BP and the disaccharide ligands mainly occurred through water-mediated hydrogen bonds. In comparison with the LNB complex, one additional hydrogen bond was found in the GNB complex. These structural characteristics of ligand binding are in agreement with the thermodynamic properties. The overall structure of GL-BP was similar to that of maltose-binding protein; however, the mode of ligand binding and the thermodynamic properties of these proteins were significantly different.

-	~~{{STRUCTURE_2z8e\| PDB=2z8e \| SCENE= }}~~	+	Structural and thermodynamic analyses of solute-binding Protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I.,Suzuki R, Wada J, Katayama T, Fushinobu S, Wakagi T, Shoun H, Sugimoto H, Tanaka A, Kumagai H, Ashida H, Kitaoka M, Yamamoto K J Biol Chem. 2008 May 9;283(19):13165-73. Epub 2008 Mar 10. PMID:18332142<ref>PMID:18332142</ref>

-	~~===The galacto-N-biose-~~/~~lacto-N-biose I-binding protein (GL-BP)~~ of the ~~ABC transporter from Bifidobacterium longum in complex with galacto-N-biose===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18332142}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[2z8e]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bifidobacterium_longum Bifidobacterium longum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA].~~	+

	==See Also==		==See Also==
	*[[ABC transporter\|ABC transporter]]		*[[ABC transporter\|ABC transporter]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018332142<~~/~~ref~~><~~ref group="xtra">PMID:017768345</ref><references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Bifidobacterium longum]]		[[Category: Bifidobacterium longum]]
	[[Category: Fushinobu, S.]]		[[Category: Fushinobu, S.]]

OCA at 09:38, 20 October 2012

OCA — Sat, 20 Oct 2012 09:38:06 GMT

←Older revision		Revision as of 09:38, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2z8e]] is a 2 chain structure ~~of [[ABC transporter]]~~ with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA].	+	[[2z8e]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA].

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

OCA at 23:30, 25 July 2012

OCA — Wed, 25 Jul 2012 23:30:28 GMT

←Older revision		Revision as of 23:30, 25 July 2012
Line 1:		Line 1:
	[[Image:2z8e.png\|left\|200px]]		[[Image:2z8e.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z8e", 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_2z8e\| PDB=2z8e \| SCENE= }}		{{STRUCTURE_2z8e\| PDB=2z8e \| SCENE= }}

	===The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose===		===The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with galacto-N-biose===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18332142}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18332142 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18332142}}		{{ABSTRACT_PUBMED_18332142}}

Line 22:		Line 11:

	==See Also==		==See Also==
-	*[[ABC transporter]]	+	*[[ABC transporter\|ABC transporter]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18332142~~</ref><ref group="xtra">PMID:~~17768345~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018332142</ref><ref group="xtra">PMID:017768345</ref><references group="xtra"/>
	[[Category: Bifidobacterium longum]]		[[Category: Bifidobacterium longum]]
	[[Category: Fushinobu, S.]]		[[Category: Fushinobu, S.]]

OCA: Protected "2z8e" [edit=sysop:move=sysop]

OCA — Sun, 26 Dec 2010 08:20:36 GMT

Protected "2z8e" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:20, 26 December 2010

OCA at 08:20, 26 December 2010

OCA — Sun, 26 Dec 2010 08:20:35 GMT

←Older revision		Revision as of 08:20, 26 December 2010
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z8e.png\|left\|200px]]		[[Image:2z8e.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~2Z8E~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA].	+	[[2z8e]] is a 2 chain structure of [[ABC transporter]] with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_longum Bifidobacterium longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8E OCA].
		+
		+	==See Also==
		+	*[[ABC transporter]]

	==Reference==		==Reference==
Line 33:		Line 35:
	[[Category: Mucin core-1]]		[[Category: Mucin core-1]]
	[[Category: Sugar binding protein]]		[[Category: Sugar binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:48:58 2009''