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| | ==Crystal structure of D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K12 complexed with D-glucitol 6-phosphate and magnesium== | | ==Crystal structure of D-Allulose 6-Phosphate 3-Epimerase from Escherichia coli K12 complexed with D-glucitol 6-phosphate and magnesium== |
| - | <StructureSection load='3ctl' size='340' side='right' caption='[[3ctl]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3ctl' size='340' side='right'caption='[[3ctl]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3ctl]] is a 6 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=3CTL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CTL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3ctl]] is a 6 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=3CTL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CTL 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=S6P:D-SORBITOL-6-PHOSPHATE'>S6P</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ct7|3ct7]]</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=S6P:D-SORBITOL-6-PHOSPHATE'>S6P</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alsE, yjcU ([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=3ctl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctl OCA], [https://pdbe.org/3ctl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ctl RCSB], [https://www.ebi.ac.uk/pdbsum/3ctl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ctl 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=3ctl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ctl OCA], [http://pdbe.org/3ctl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ctl RCSB], [http://www.ebi.ac.uk/pdbsum/3ctl PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/ALSE_ECOLI ALSE_ECOLI]] Catalyzes the reversible epimerization of D-allulose 6-phosphate to D-fructose 6-phosphate. Can also catalyze with lower efficiency the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate.<ref>PMID:18700786</ref> <ref>PMID:9401019</ref> | + | [https://www.uniprot.org/uniprot/ALSE_ECOLI ALSE_ECOLI] Catalyzes the reversible epimerization of D-allulose 6-phosphate to D-fructose 6-phosphate. Can also catalyze with lower efficiency the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate.<ref>PMID:18700786</ref> <ref>PMID:9401019</ref> |
| | == 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/ct/3ctl_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ct/3ctl_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: Almo, S C]] | + | [[Category: Large Structures]] |
| - | [[Category: Chan, K K]] | + | [[Category: Almo SC]] |
| - | [[Category: Fedorov, A A]] | + | [[Category: Chan KK]] |
| - | [[Category: Fedorov, E V]] | + | [[Category: Fedorov AA]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Fedorov EV]] |
| - | [[Category: Carbohydrate metabolism]] | + | [[Category: Gerlt JA]] |
| - | [[Category: D-allulose 6-phosphate 3-epimerase]]
| + | |
| - | [[Category: D-glucitol 6-phosphate]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| Structural highlights
Function
ALSE_ECOLI Catalyzes the reversible epimerization of D-allulose 6-phosphate to D-fructose 6-phosphate. Can also catalyze with lower efficiency the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate.[1] [2]
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
Enzymes that share the (beta/alpha) 8-barrel fold catalyze a diverse range of reactions. Many utilize phosphorylated substrates and share a conserved C-terminal (beta/alpha) 2-quarter barrel subdomain that provides a binding motif for the dianionic phosphate group. We recently reported functional and structural studies of d-ribulose 5-phosphate 3-epimerase (RPE) from Streptococcus pyogenes that catalyzes the equilibration of the pentulose 5-phosphates d-ribulose 5-phosphate and d-xylulose 5-phosphate in the pentose phosphate pathway [J. Akana, A. A. Fedorov, E. Fedorov, W. R. P. Novack, P. C. Babbitt, S. C. Almo, and J. A. Gerlt (2006) Biochemistry 45, 2493-2503]. We now report functional and structural studies of d-allulose 6-phosphate 3-epimerase (ALSE) from Escherichia coli K-12 that catalyzes the equilibration of the hexulose 6-phosphates d-allulose 6-phosphate and d-fructose 6-phosphate in a catabolic pathway for d-allose. ALSE and RPE prefer their physiological substrates but are promiscuous for each other's substrate. The active sites (RPE complexed with d-xylitol 5-phosphate and ALSE complexed with d-glucitol 6-phosphate) are superimposable (as expected from their 39% sequence identity), with the exception of the phosphate binding motif. The loop following the eighth beta-strand in ALSE is one residue longer than the homologous loop in RPE, so the binding site for the hexulose 6-phosphate substrate/product in ALSE is elongated relative to that for the pentulose 5-phosphate substrate/product in RPE. We constructed three single-residue deletion mutants of the loop in ALSE, DeltaT196, DeltaS197 and DeltaG198, to investigate the structural bases for the differing substrate specificities; for each, the promiscuity is altered so that d-ribulose 5-phosphate is the preferred substrate. The changes in k cat/ K m are dominated by changes in k cat, suggesting that substrate discrimination results from differential transition state stabilization. In both ALSE and RPE, the phosphate group hydrogen bonds not only with the conserved motif but also with an active site loop following the sixth beta-strand, providing a potential structural mechanism for coupling substrate binding with catalysis.
Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12.,Chan KK, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA Biochemistry. 2008 Sep 9;47(36):9608-17. Epub 2008 Aug 14. PMID:18700786[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Chan KK, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12. Biochemistry. 2008 Sep 9;47(36):9608-17. Epub 2008 Aug 14. PMID:18700786 doi:10.1021/bi800821v
- ↑ Kim C, Song S, Park C. The D-allose operon of Escherichia coli K-12. J Bacteriol. 1997 Dec;179(24):7631-7. PMID:9401019
- ↑ Chan KK, Fedorov AA, Fedorov EV, Almo SC, Gerlt JA. Structural basis for substrate specificity in phosphate binding (beta/alpha)8-barrels: D-allulose 6-phosphate 3-epimerase from Escherichia coli K-12. Biochemistry. 2008 Sep 9;47(36):9608-17. Epub 2008 Aug 14. PMID:18700786 doi:10.1021/bi800821v
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