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6zll

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Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Galacturonic acid and NAD

Structural highlights

6zll is a 4 chain structure with sequence from Bacillus cereus HuA2-4. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.85Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

UDP-glucuronic acid is converted to UDP-galacturonic acid en route to a variety of sugar-containing metabolites. This reaction is performed by a NAD(+)-dependent epimerase belonging to the short-chain dehydrogenase/reductase family. We present several high-resolution crystal structures of the UDP-glucuronic acid epimerase from Bacillus cereus The geometry of the substrate-NAD(+) interactions is finely arranged to promote hydride transfer. The exquisite complementarity between glucuronic acid and its binding site is highlighted by the observation that the unligated cavity is occupied by a cluster of ordered waters whose positions overlap the polar groups of the sugar substrate. Co-crystallization experiments led to a structure where substrate- and product-bound enzymes coexist within the same crystal. This equilibrium structure reveals the basis for a "swing & flip" rotation of the pro-chiral 4-keto-hexose-uronic acid intermediate that results from glucuronic acid oxidation, placing the C4' atom in position for receiving a hydride ion on the opposite side of the sugar ring. The product-bound active site is almost identical to that of the substrate-bound structure and satisfies all hydrogen-bonding requirements of the ligand. The structure of the apo-enzyme together with kinetic isotope effect and mutagenesis experiments further outlines a few flexible loops that exist in discrete conformations, imparting structural malleability required for ligand rotation while avoiding leakage of the catalytic intermediate and/or side-reactions. These data highlight the double nature of the enzymatic mechanism: the active site features a high degree of precision in substrate recognition combined with the flexibility required for intermediate rotation.

Crystallographic snapshots of UDP-glucuronic acid 4-epimeraseligand binding, rotation and reduction.,Iacovino LG, Savino S, Borg AJE, Binda C, Nidetzky B, Mattevi A J Biol Chem. 2020 Jul 13. pii: RA120.014692. doi: 10.1074/jbc.RA120.014692. PMID:32661196^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Iacovino LG, Savino S, Borg AJE, Binda C, Nidetzky B, Mattevi A. Crystallographic snapshots of UDP-glucuronic acid 4-epimeraseligand binding, rotation and reduction. J Biol Chem. 2020 Jul 13. pii: RA120.014692. doi: 10.1074/jbc.RA120.014692. PMID:32661196 doi:http://dx.doi.org/10.1074/jbc.RA120.014692

1 Structural highlights
2 Publication Abstract from PubMed
3 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

Categories: Bacillus cereus HuA2-4 | Large Structures | Iacovino LG | Mattevi A | Savino S

@@ Line 3: / Line 3: @@
 <StructureSection load='6zll' size='340' side='right'caption='[[6zll]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6zll]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_cereus_hua2-4 Bacillus cereus hua2-4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZLL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6ZLL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6zll]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_cereus_HuA2-4 Bacillus cereus HuA2-4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZLL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZLL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UGB:(2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-3,4,5-TRIHYDROXY-OXANE-2-CARBOXYLIC+ACID'>UGB</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]] 1.85&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IG7_05634 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1053203 Bacillus cereus HuA2-4])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UGB:(2S,3R,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-DIOXOPYRIMIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL]OXY-HYDROXY-PHOSPHORYL]OXY-3,4,5-TRIHYDROXY-OXANE-2-CARBOXYLIC+ACID'>UGB</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6zll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zll OCA], [http://pdbe.org/6zll PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6zll RCSB], [http://www.ebi.ac.uk/pdbsum/6zll PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6zll ProSAT]</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=6zll FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zll OCA], [https://pdbe.org/6zll PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zll RCSB], [https://www.ebi.ac.uk/pdbsum/6zll PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zll ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 21: / Line 21: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus cereus hua2-4]]
+[[Category: Bacillus cereus HuA2-4]]
 [[Category: Large Structures]]
-[[Category: Iacovino, L G]]
+[[Category: Iacovino LG]]
-[[Category: Mattevi, A]]
+[[Category: Mattevi A]]
-[[Category: Savino, S]]
+[[Category: Savino S]]
-[[Category: Epimerase]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]
-[[Category: Udp-galacturonic acid]]
-[[Category: Udp-sugar binding protein]]

6zll

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Current revision

Crystal Structure of UDP-Glucuronic acid 4-epimerase from Bacillus cereus in complex with UDP-Galacturonic acid and NAD

Structural highlights

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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