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| | <StructureSection load='2hk1' size='340' side='right'caption='[[2hk1]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='2hk1' size='340' side='right'caption='[[2hk1]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2hk1]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_radiobacter"_(beijerinck_and_van_delden_1902)_bergey_et_al._1934 "achromobacter radiobacter" (beijerinck and van delden 1902) bergey et al. 1934]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2HK1 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2hk1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2HK1 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FUD:D-FRUCTOSE'>FUD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FUD:D-FRUCTOSE'>FUD</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2hk0|2hk0]]</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=2hk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk1 OCA], [https://pdbe.org/2hk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2hk1 RCSB], [https://www.ebi.ac.uk/pdbsum/2hk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk1 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=2hk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2hk1 OCA], [http://pdbe.org/2hk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2hk1 RCSB], [http://www.ebi.ac.uk/pdbsum/2hk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2hk1 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/DPES_AGRFC DPES_AGRFC] Involved in the biosynthesis of D-psicose. Catalyzes the reversible epimerization of D-fructose at the C3 position to yield D-psicose. The enzyme is highly specific for D-psicose and shows very low activity with D-tagatose. The substrate specificity decreases in the following order: D-fructose, D-tagatose, D-ribulose, D-xylulose, and D-sorbose. It shows a higher level of activity for cis ketoses than for trans-ketoses.<ref>PMID:16461638</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hk/2hk1_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hk/2hk1_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Agrobacterium tumefaciens]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Cha, S S]] | + | [[Category: Cha SS]] |
| - | [[Category: Kim, H J]] | + | [[Category: Kim HJ]] |
| - | [[Category: Kim, K]] | + | [[Category: Kim K]] |
| - | [[Category: Oh, D K]] | + | [[Category: Oh DK]] |
| - | [[Category: Rhee, S]] | + | [[Category: Rhee S]] |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Tim-barrel]]
| + | |
| Structural highlights
Function
DPES_AGRFC Involved in the biosynthesis of D-psicose. Catalyzes the reversible epimerization of D-fructose at the C3 position to yield D-psicose. The enzyme is highly specific for D-psicose and shows very low activity with D-tagatose. The substrate specificity decreases in the following order: D-fructose, D-tagatose, D-ribulose, D-xylulose, and D-sorbose. It shows a higher level of activity for cis ketoses than for trans-ketoses.[1]
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
D-psicose, a rare sugar produced by the enzymatic reaction of D-tagatose 3-epimerase (DTEase), has been used extensively for the bioproduction of various rare carbohydrates. Recently characterized D-psicose 3-epimerase (DPEase) from Agrobacterium tumefaciens was found to belong to the DTEase family and to catalyze the interconversion of D-fructose and D-psicose by epimerizing the C-3 position, with marked efficiency for D-psicose. The crystal structures of DPEase and its complex with the true substrate D-fructose were determined; DPEase is a tetramer and each monomer belongs to a TIM-barrel fold. The active site in each subunit is distinct from that of other TIM-barrel enzymes, which use phosphorylated ligands as the substrate. It contains a metal ion with octahedral coordination to two water molecules and four residues that are absolutely conserved across the DTEase family. Upon binding of D-fructose, the substrate displaces water molecules in the active site, with a conformation mimicking the intermediate cis-enediolate. Subsequently, Trp112 and Pro113 in the beta4-alpha4 loop undergo significant structural changes, sealing off the active site. Structural evidence and site-directed mutagenesis of the putative catalytic residues suggest that the metal ion plays a pivotal role in catalysis by anchoring the bound D-fructose, and Glu150 and Glu244 carry out an epimerization reaction at the C-3 position.
Crystal structure of D-psicose 3-epimerase from Agrobacterium tumefaciens and its complex with true substrate D-fructose: a pivotal role of metal in catalysis, an active site for the non-phosphorylated substrate, and its conformational changes.,Kim K, Kim HJ, Oh DK, Cha SS, Rhee S J Mol Biol. 2006 Sep 1;361(5):920-31. Epub 2006 Jul 28. PMID:16876192[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kim HJ, Hyun EK, Kim YS, Lee YJ, Oh DK. Characterization of an Agrobacterium tumefaciens D-psicose 3-epimerase that converts D-fructose to D-psicose. Appl Environ Microbiol. 2006 Feb;72(2):981-5. PMID:16461638 doi:10.1128/AEM.72.2.981-985.2006
- ↑ Kim K, Kim HJ, Oh DK, Cha SS, Rhee S. Crystal structure of D-psicose 3-epimerase from Agrobacterium tumefaciens and its complex with true substrate D-fructose: a pivotal role of metal in catalysis, an active site for the non-phosphorylated substrate, and its conformational changes. J Mol Biol. 2006 Sep 1;361(5):920-31. Epub 2006 Jul 28. PMID:16876192 doi:10.1016/j.jmb.2006.06.069
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