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5gqc

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==Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, ligand-free form==
==Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, ligand-free form==
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<StructureSection load='5gqc' size='340' side='right' caption='[[5gqc]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
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<StructureSection load='5gqc' size='340' side='right'caption='[[5gqc]], [[Resolution|resolution]] 2.36&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5gqc]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GQC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5GQC FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5gqc]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._longum Bifidobacterium longum subsp. longum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5GQC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GQC FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.36&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5gqf|5gqf]], [[5gqg|5gqg]]</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Lacto-N-biosidase Lacto-N-biosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.140 3.2.1.140] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5gqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gqc OCA], [https://pdbe.org/5gqc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gqc RCSB], [https://www.ebi.ac.uk/pdbsum/5gqc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gqc ProSAT]</span></td></tr>
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<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=5gqc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gqc OCA], [http://pdbe.org/5gqc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5gqc RCSB], [http://www.ebi.ac.uk/pdbsum/5gqc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5gqc ProSAT]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A024QYS6_BIFLN A0A024QYS6_BIFLN]
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Breast-fed infants generally have a bifidobacteria-rich microbiota with recent studies indicating that human milk oligosaccharides (HMOs) selectively promote bifidobacterial growth. Bifidobacterium bifidum possesses a glycoside hydrolase family 20 lacto-N-biosidase for liberating lacto-N-biose I from lacto-N-tetraose, an abundant HMO unique to human milk, while Bifidobacterium longum subsp. longum has a non-classified enzyme (LnbX). Here, we determined the crystal structure of the catalytic domain of LnbX and provide evidence for creation of a novel glycoside hydrolase family, GH136. The structure, in combination with inhibition and mutation studies, provides insight into the molecular mechanism and broader substrate specificity of this enzyme. Moreover, through genetic studies, we show that lnbX is indispensable for B. longum growth on lacto-N-tetraose and is a key genetic factor for persistence in the gut of breast-fed infants. Overall, this study reveals possible evolutionary routes for the emergence of symbiosis between humans and bifidobacterial species in the infant gut.
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Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum.,Yamada C, Gotoh A, Sakanaka M, Hattie M, Stubbs KA, Katayama-Ikegami A, Hirose J, Kurihara S, Arakawa T, Kitaoka M, Okuda S, Katayama T, Fushinobu S Cell Chem Biol. 2017 Apr 4. pii: S2451-9456(17)30095-8. doi:, 10.1016/j.chembiol.2017.03.012. PMID:28392148<ref>PMID:28392148</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5gqc" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Lacto-N-biosidase]]
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[[Category: Bifidobacterium longum subsp. longum]]
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[[Category: Arakawa, T]]
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[[Category: Large Structures]]
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[[Category: Fushinobu, S]]
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[[Category: Arakawa T]]
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[[Category: Katayama, T]]
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[[Category: Fushinobu S]]
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[[Category: Yamada, C]]
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[[Category: Katayama T]]
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[[Category: Beta-helix]]
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[[Category: Yamada C]]
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[[Category: Hydrolase]]
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Current revision

Crystal structure of lacto-N-biosidase LnbX from Bifidobacterium longum subsp. longum, ligand-free form

PDB ID 5gqc

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