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| | <StructureSection load='5bxt' size='340' side='right'caption='[[5bxt]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='5bxt' size='340' side='right'caption='[[5bxt]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5bxt]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifidobacterium_bifidum_jcm_1254 Bifidobacterium bifidum jcm 1254]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BXT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5bxt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_bifidum_JCM_1254 Bifidobacterium bifidum JCM 1254]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BXT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4WS:N-{[(1R,2R,3R,7S,7AR)-1,2,7-TRIHYDROXYHEXAHYDRO-1H-PYRROLIZIN-3-YL]METHYL}ACETAMIDE'>4WS</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4WS:N-{[(1R,2R,3R,7S,7AR)-1,2,7-TRIHYDROXYHEXAHYDRO-1H-PYRROLIZIN-3-YL]METHYL}ACETAMIDE'>4WS</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5bxp|5bxp]], [[5bxs|5bxs]], [[5bxr|5bxr]]</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=5bxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bxt OCA], [https://pdbe.org/5bxt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bxt RCSB], [https://www.ebi.ac.uk/pdbsum/5bxt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bxt ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lnbB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=398514 Bifidobacterium bifidum JCM 1254])</td></tr>
| + | |
| - | <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>
| + | |
| - | <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=5bxt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bxt OCA], [http://pdbe.org/5bxt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bxt RCSB], [http://www.ebi.ac.uk/pdbsum/5bxt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bxt ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/LNBB_BIFB1 LNBB_BIFB1] Present in the infant gut, this enzyme is involved in the assimilation of type-1 human milk oligosaccharides (HMOs). It hydrolyzes via a retaining mechanism the beta-D-GlcNAc-(1->3)-beta-D-Gal linkage in lacto-N-tetraose (LNT or beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc), an abundant HMO unique to human breast milk, releasing lacto-N-biose (LNB or beta-D-Gal-(1->3)-D-GlcNAc) and lactose (PubMed:18469123, PubMed:23479733). Is a key enzymatic factor for growth and proliferation of B.bifidum in the gut ecosystem of breast-fed infants (Probable). Has substrate preference for unmodified beta-linked LNB since it does not hydrolyze the fucosylated forms of lacto-N-tetraose (lacto-N-fucopentaose I and II) or lacto-N-neotetraose. Is also able to display transglycosylation activity in vitro (PubMed:18469123).<ref>PMID:18469123</ref> <ref>PMID:23479733</ref> <ref>PMID:23479733</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bifidobacterium bifidum jcm 1254]] | + | [[Category: Bifidobacterium bifidum JCM 1254]] |
| - | [[Category: Lacto-N-biosidase]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Arakawa, T]] | + | [[Category: Arakawa T]] |
| - | [[Category: Fushinobu, S]] | + | [[Category: Fushinobu S]] |
| - | [[Category: Ito, T]] | + | [[Category: Ito T]] |
| - | [[Category: Distal gut]]
| + | |
| - | [[Category: Human milk oligosaccharide]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Inhibitor]]
| + | |
| - | [[Category: Tim barrel]]
| + | |
| Structural highlights
Function
LNBB_BIFB1 Present in the infant gut, this enzyme is involved in the assimilation of type-1 human milk oligosaccharides (HMOs). It hydrolyzes via a retaining mechanism the beta-D-GlcNAc-(1->3)-beta-D-Gal linkage in lacto-N-tetraose (LNT or beta-D-Gal-(1->3)-beta-D-GlcNAc-(1->3)-beta-D-Gal-(1->4)-D-Glc), an abundant HMO unique to human breast milk, releasing lacto-N-biose (LNB or beta-D-Gal-(1->3)-D-GlcNAc) and lactose (PubMed:18469123, PubMed:23479733). Is a key enzymatic factor for growth and proliferation of B.bifidum in the gut ecosystem of breast-fed infants (Probable). Has substrate preference for unmodified beta-linked LNB since it does not hydrolyze the fucosylated forms of lacto-N-tetraose (lacto-N-fucopentaose I and II) or lacto-N-neotetraose. Is also able to display transglycosylation activity in vitro (PubMed:18469123).[1] [2] [3]
Publication Abstract from PubMed
The synthesis of potent inhibitors for lacto-N-biosidases and X-ray structural characterization of these compounds in complex with BbLNBase is described.
Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis.,Hattie M, Ito T, Debowski AW, Arakawa T, Katayama T, Yamamoto K, Fushinobu S, Stubbs KA Chem Commun (Camb). 2015 Aug 27. PMID:26312778[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Wada J, Ando T, Kiyohara M, Ashida H, Kitaoka M, Yamaguchi M, Kumagai H, Katayama T, Yamamoto K. Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure. Appl Environ Microbiol. 2008 Jul;74(13):3996-4004. doi: 10.1128/AEM.00149-08., Epub 2008 May 9. PMID:18469123 doi:http://dx.doi.org/10.1128/AEM.00149-08
- ↑ Ito T, Katayama T, Hattie M, Sakurama H, Wada J, Suzuki R, Ashida H, Wakagi T, Yamamoto K, Stubbs KA, Fushinobu S. Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum. J Biol Chem. 2013 Apr 26;288(17):11795-806. doi: 10.1074/jbc.M112.420109. Epub, 2013 Mar 11. PMID:23479733 doi:10.1074/jbc.M112.420109
- ↑ Ito T, Katayama T, Hattie M, Sakurama H, Wada J, Suzuki R, Ashida H, Wakagi T, Yamamoto K, Stubbs KA, Fushinobu S. Crystal structures of a glycoside hydrolase family 20 lacto-N-biosidase from Bifidobacterium bifidum. J Biol Chem. 2013 Apr 26;288(17):11795-806. doi: 10.1074/jbc.M112.420109. Epub, 2013 Mar 11. PMID:23479733 doi:10.1074/jbc.M112.420109
- ↑ Hattie M, Ito T, Debowski AW, Arakawa T, Katayama T, Yamamoto K, Fushinobu S, Stubbs KA. Gaining insight into the catalysis by GH20 lacto-N-biosidase using small molecule inhibitors and structural analysis. Chem Commun (Camb). 2015 Aug 27. PMID:26312778 doi:http://dx.doi.org/10.1039/c5cc05494j
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