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| | ==Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (form B) complex with Zn2+== | | ==Crystal Structure of L-xylulose-5-phosphate 3-epimerase UlaE (form B) complex with Zn2+== |
| - | <StructureSection load='3cqj' size='340' side='right' caption='[[3cqj]], [[Resolution|resolution]] 2.04Å' scene=''> | + | <StructureSection load='3cqj' size='340' side='right'caption='[[3cqj]], [[Resolution|resolution]] 2.04Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3cqj]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CQJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3cqj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CQJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CQJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.04Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cqh|3cqh]], [[3cqi|3cqi]], [[3cqk|3cqk]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ulaE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=3cqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cqj OCA], [https://pdbe.org/3cqj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cqj RCSB], [https://www.ebi.ac.uk/pdbsum/3cqj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cqj ProSAT], [https://www.topsan.org/Proteins/BSGI/3cqj TOPSAN]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-ribulose-5-phosphate_3-epimerase L-ribulose-5-phosphate 3-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.22 5.1.3.22] </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=3cqj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cqj OCA], [http://pdbe.org/3cqj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cqj RCSB], [http://www.ebi.ac.uk/pdbsum/3cqj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cqj ProSAT], [http://www.topsan.org/Proteins/BSGI/3cqj TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ULAE_ECO57 ULAE_ECO57]] Catalyzes the isomerization of L-xylulose-5-phosphate to L-ribulose-5-phosphate. Is involved in the anaerobic L-ascorbate utilization (By similarity). | + | [https://www.uniprot.org/uniprot/ULAE_ECO57 ULAE_ECO57] Catalyzes the isomerization of L-xylulose-5-phosphate to L-ribulose-5-phosphate. Is involved in the anaerobic L-ascorbate utilization (By similarity). |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cq/3cqj_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cq/3cqj_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[Category: Escherichia coli]] |
| - | [[Category: L-ribulose-5-phosphate 3-epimerase]] | + | [[Category: Large Structures]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Cygler M]] |
| - | [[Category: Cygler, M]] | + | [[Category: Matte A]] |
| - | [[Category: Matte, A]] | + | [[Category: Shi R]] |
| - | [[Category: Shi, R]] | + | |
| - | [[Category: Bsgi]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Phosphate-binding motif]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| Structural highlights
Function
ULAE_ECO57 Catalyzes the isomerization of L-xylulose-5-phosphate to L-ribulose-5-phosphate. Is involved in the anaerobic L-ascorbate utilization (By similarity).
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Three catabolic enzymes, UlaD, UlaE, and UlaF, are involved in a pathway leading to fermentation of l-ascorbate under anaerobic conditions. UlaD catalyzes a beta-keto acid decarboxylation reaction to produce l-xylulose-5-phosphate, which undergoes successive epimerization reactions with UlaE (l-xylulose-5-phosphate 3-epimerase) and UlaF (l-ribulose-5-phosphate 4-epimerase), yielding d-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway. We describe here crystallographic studies of UlaE from Escherichia coli O157:H7 that complete the structural characterization of this pathway. UlaE has a triosephosphate isomerase (TIM) barrel fold and forms dimers. The active site is located at the C-terminal ends of the parallel beta-strands. The enzyme binds Zn(2+), which is coordinated by Glu155, Asp185, His211, and Glu251. We identified a phosphate-binding site formed by residues from the beta1/alpha1 loop and alpha3' helix in the N-terminal region. This site differs from the well-characterized phosphate-binding motif found in several TIM barrel superfamilies that is located at strands beta7 and beta8. The intrinsic flexibility of the active site region is reflected by two different conformations of loops forming part of the substrate-binding site. Based on computational docking of the l-xylulose 5-phosphate substrate to UlaE and structural similarities of the active site of this enzyme to the active sites of other epimerases, a metal-dependent epimerization mechanism for UlaE is proposed, and Glu155 and Glu251 are implicated as catalytic residues. Mutation and activity measurements for structurally equivalent residues in related epimerases supported this mechanistic proposal.
Structure of L-Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic L-Ascorbate Utilization Pathway of Escherichia coli: Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold.,Shi R, Pineda M, Ajamian E, Cui Q, Matte A, Cygler M J Bacteriol. 2008 Dec;190(24):8137-44. Epub 2008 Oct 10. PMID:18849419[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shi R, Pineda M, Ajamian E, Cui Q, Matte A, Cygler M. Structure of L-Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic L-Ascorbate Utilization Pathway of Escherichia coli: Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold. J Bacteriol. 2008 Dec;190(24):8137-44. Epub 2008 Oct 10. PMID:18849419 doi:JB.01049-08
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