2z8d: Difference between revisions

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 ==The galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum in complex with lacto-N-biose==
-<StructureSection load='2z8d' size='340' side='right' caption='[[2z8d]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+<StructureSection load='2z8d' size='340' side='right'caption='[[2z8d]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2z8d]] 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=2Z8D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z8D FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2z8d]] 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=2Z8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z8D 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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.85&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2z8e|2z8e]], [[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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gltA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216816 AS 1.2186])</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=2z8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8d OCA], [https://pdbe.org/2z8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z8d RCSB], [https://www.ebi.ac.uk/pdbsum/2z8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8d ProSAT]</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=2z8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8d OCA], [http://pdbe.org/2z8d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z8d RCSB], [http://www.ebi.ac.uk/pdbsum/2z8d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8d ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A8W790_BIFLN A8W790_BIFLN]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / 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=2z8d 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.
-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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2z8d" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[ABC transporter|ABC transporter]]
+*[[ABC transporter 3D structures|ABC transporter 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: As 1 2186]]
+[[Category: Bifidobacterium longum]]
-[[Category: Fushinobu, S]]
+[[Category: Large Structures]]
-[[Category: Katayama, T]]
+[[Category: Fushinobu S]]
-[[Category: Suzuki, R]]
+[[Category: Katayama T]]
-[[Category: Wada, J]]
+[[Category: Suzuki R]]
-[[Category: Abc transporter]]
+[[Category: Wada J]]
-[[Category: Human milk oligosacchalide]]
-[[Category: Mucin core-1]]
-[[Category: Sugar binding protein]]