2zuu
From Proteopedia
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==Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc== | ==Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc== | ||
| - | <StructureSection load='2zuu' size='340' side='right' caption='[[2zuu]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='2zuu' size='340' side='right'caption='[[2zuu]], [[Resolution|resolution]] 2.30Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[2zuu]] is a 4 chain structure with sequence from [ | + | <table><tr><td colspan='2'>[[2zuu]] is a 4 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=2ZUU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZUU FirstGlance]. <br> |
| - | </td></tr><tr><td class="sblockLbl"><b>[[ | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr> | |
| - | <tr><td class="sblockLbl"><b>[[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zuu OCA], [https://pdbe.org/2zuu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zuu RCSB], [https://www.ebi.ac.uk/pdbsum/2zuu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zuu ProSAT]</span></td></tr> |
| - | < | + | </table> |
| - | <tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | == Function == |
| - | <table> | + | [https://www.uniprot.org/uniprot/LNPA_BIFL2 LNPA_BIFL2] Reversibly phosphorolyzes lacto-N-biose to Gal1-P and N-acetylglucosamine (GlcNAc) and galacto-N-biose to Gal1-P and N-acetylgalactosamine (GalNAc). Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria.<ref>PMID:15933016</ref> <ref>PMID:17720833</ref> <ref>PMID:19124470</ref> |
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zu/2zuu_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zu/2zuu_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> | ||
</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/ | + | </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=2zuu ConSurf]. |
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Galacto-N-biose/lacto-N-biose I phosphorylase (GLNBP) from Bifidobacterium longum, a key enzyme for intestinal growth, phosphorolyses galacto-N-biose and lacto-N-biose I with anomeric inversion. GLNBP homologues are often found in human pathogenic and commensal bacteria, and their substrate specificities potentially define the nutritional acquisition ability of these microbes in their habitat. We report the crystal structures of GLNBP in five different ligand-binding forms. This is the first three-dimensional structure of glycoside hydrolase (GH) family 112. The GlcNAc- and GalNAc-bound forms provide structural insights into distinct substrate preferences of GLNBP and its homologues from pathogens. The catalytic domain consists of a partially broken TIM barrel fold that is structurally similar to a thermophilic beta-galactosidase, strongly supporting the current classification of GLNBP homologues as one of the GH families. Anion binding induces a large conformational change by rotating a half-unit of the barrel. This is an unusual example of molecular adaptation of a TIM barrel scaffold to substrates. | ||
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| - | The crystal structure of galacto-N-biose/lacto-N-biose I phosphorylase: a large deformation of a TIM barrel scaffold.,Hidaka M, Nishimoto M, Kitaoka M, Wakagi T, Shoun H, Fushinobu S J Biol Chem. 2009 Mar 13;284(11):7273-83. Epub 2009 Jan 5. PMID:19124470<ref>PMID:19124470</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: 1,3-beta-galactosyl-N-acetylhexosamine phosphorylase]] | ||
[[Category: Bifidobacterium longum]] | [[Category: Bifidobacterium longum]] | ||
| - | [[Category: Fushinobu | + | [[Category: Large Structures]] |
| - | [[Category: Hidaka | + | [[Category: Fushinobu S]] |
| - | [[Category: Kitaoka | + | [[Category: Hidaka M]] |
| - | [[Category: Nishimoto | + | [[Category: Kitaoka M]] |
| - | [[Category: Shoun | + | [[Category: Nishimoto M]] |
| - | [[Category: Wakagi | + | [[Category: Shoun H]] |
| - | + | [[Category: Wakagi T]] | |
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Current revision
Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc
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