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| | <StructureSection load='6k0g' size='340' side='right'caption='[[6k0g]], [[Resolution|resolution]] 1.80Å' scene=''> | | <StructureSection load='6k0g' size='340' side='right'caption='[[6k0g]], [[Resolution|resolution]] 1.80Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6k0g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bifl2 Bifl2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6k0g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bifidobacterium_longum_subsp._longum_JCM_1217 Bifidobacterium longum subsp. longum JCM 1217]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6K0G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K0G FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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]] 1.8Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">lnpD, BLLJ_1620 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=565042 BIFL2])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=6k0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0g OCA], [https://pdbe.org/6k0g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k0g RCSB], [https://www.ebi.ac.uk/pdbsum/6k0g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0g 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=6k0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0g OCA], [http://pdbe.org/6k0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0g RCSB], [http://www.ebi.ac.uk/pdbsum/6k0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0g ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/GALE_BIFL2 GALE_BIFL2]] Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. 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:17720833</ref> | + | [https://www.uniprot.org/uniprot/GALE_BIFL2 GALE_BIFL2] Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. 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:17720833</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6k0g" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6k0g" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[UDP-galactose 4-epimerase|UDP-galactose 4-epimerase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bifl2]] | + | [[Category: Bifidobacterium longum subsp. longum JCM 1217]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: UDP-glucose 4-epimerase]]
| + | [[Category: Arakawa T]] |
| - | [[Category: Arakawa, T]] | + | [[Category: Fushinobu S]] |
| - | [[Category: Fushinobu, S]] | + | [[Category: Kitaoka M]] |
| - | [[Category: Kitaoka, M]] | + | [[Category: Nam Y-W]] |
| - | [[Category: Nam, Y W]] | + | [[Category: Nishimoto M]] |
| - | [[Category: Nishimoto, M]] | + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
GALE_BIFL2 Involved in the metabolism of galactose. Catalyzes the conversion of UDP-galactose (UDP-Gal) to UDP-glucose (UDP-Glc) through a mechanism involving the transient reduction of NAD. Can also epimerize UDP-GalNAc to UDP-GlcNAc. Involved in the lacto-N-biose I/galacto-N-biose (LNB/GNB) degradation pathway, which is important for host intestinal colonization by bifidobacteria.[1]
Publication Abstract from PubMed
Infant gut-associated bifidobacteria has a metabolic pathway that specifically utilizes lacto-N-biose I (Gal-beta1,3-GlcNAc) and galacto-N-biose (Gal-beta1,3-GalNAc) from human milk and mucin glycans. UDP-glucose 4-epimerase (GalE) from Bifidobacterium longum (bGalE) catalyzes epimerization reactions of UDP-Gal into UDP-Glc and UDP-GalNAc into UDP-GlcNAc with the same level of activity that is required to send galacto-hexoses into glycolysis. Here, we determined the crystal structures of bGalE in three ternary complex forms: NAD(+)/UDP, NAD(+)/UDP-GlcNAc, and NAD(+)/UDP-Glc. The broad specificity of bGalE was explained by structural features of the binding pocket for the N-acetyl or C2 hydroxy group of the substrate. Asn200 is located in a pocket of the C2 group, and its side chain adopts different conformations in the complex structures with UDP-Glc and UDP-GlcNAc. On the other side, Cys299 forms a large pocket for the C5 sugar ring atom. The flexible C2 pocket and the large C5 pocket of bGalE are suitable for accommodating both the hydroxy and N-acetyl groups of the substrate during sugar ring rotation in the catalytic cycle. The substrate specificity and active site structure of bGalE were distinct from those of Esherichia coli GalE but similar to those of human GalE.
Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum.,Nam YW, Nishimoto M, Arakawa T, Kitaoka M, Fushinobu S Sci Rep. 2019 Jul 31;9(1):11081. doi: 10.1038/s41598-019-47591-w. PMID:31366978[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Nishimoto M, Kitaoka M. Identification of N-acetylhexosamine 1-kinase in the complete lacto-N-biose I/galacto-N-biose metabolic pathway in Bifidobacterium longum. Appl Environ Microbiol. 2007 Oct;73(20):6444-9. Epub 2007 Aug 24. PMID:17720833 doi:http://dx.doi.org/10.1128/AEM.01425-07
- ↑ Nam YW, Nishimoto M, Arakawa T, Kitaoka M, Fushinobu S. Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum. Sci Rep. 2019 Jul 31;9(1):11081. doi: 10.1038/s41598-019-47591-w. PMID:31366978 doi:http://dx.doi.org/10.1038/s41598-019-47591-w
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