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6k0h

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Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc

Structural highlights

6k0h is a 1 chain structure with sequence from Bifidobacterium longum subsp. longum JCM 1217. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6k0h"

@@ Line 3: / Line 3: @@
 <StructureSection load='6k0h' size='340' side='right'caption='[[6k0h]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6k0h]] 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=6K0H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6K0H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6k0h]] 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=6K0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6K0H 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</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]] 2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">galE, 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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=UD1:URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE'>UD1</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=6k0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0h OCA], [https://pdbe.org/6k0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6k0h RCSB], [https://www.ebi.ac.uk/pdbsum/6k0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0h 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=6k0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6k0h OCA], [http://pdbe.org/6k0h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6k0h RCSB], [http://www.ebi.ac.uk/pdbsum/6k0h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6k0h ProSAT]</span></td></tr>
 </table>
 == 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;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 19: @@
 </div>
 <div class="pdbe-citations 6k0h" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[UDP-galactose 4-epimerase|UDP-galactose 4-epimerase]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bifl2]]
+[[Category: Bifidobacterium longum subsp. longum JCM 1217]]
 [[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: Hydrolase]]
-[[Category: Isomerase]]
-[[Category: Rossmann fold]]

6k0h

From Proteopedia

Current revision

Crystal Structure of UDP-glucose 4-epimerase from Bifidobacterium longum in complex with NAD+ and UDP-GlcNAc

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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