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| | ==Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with Mg++ and meso-tartrate== | | ==Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with Mg++ and meso-tartrate== |
| - | <StructureSection load='2dw7' size='340' side='right' caption='[[2dw7]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='2dw7' size='340' side='right'caption='[[2dw7]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2dw7]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/"rhizobacterium_japonicum"_kirchner_1896 "rhizobacterium japonicum" kirchner 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DW7 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2dw7]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DW7 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=SRT:S,R+MESO-TARTARIC+ACID'>SRT</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]] 2.5Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1tzz|1tzz]], [[2dw6|2dw6]]</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=SRT:S,R+MESO-TARTARIC+ACID'>SRT</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/D(-)-tartrate_dehydratase D(-)-tartrate dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.81 4.2.1.81] </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=2dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw7 OCA], [https://pdbe.org/2dw7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dw7 RCSB], [https://www.ebi.ac.uk/pdbsum/2dw7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw7 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=2dw7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw7 OCA], [http://pdbe.org/2dw7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dw7 RCSB], [http://www.ebi.ac.uk/pdbsum/2dw7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dw7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TARD_BRADU TARD_BRADU]] Catalyzes the dehydration of D-tartrate to oxaloacetate.<ref>PMID:17144653</ref> | + | [https://www.uniprot.org/uniprot/TARD_BRADU TARD_BRADU] Catalyzes the dehydration of D-tartrate to oxaloacetate.<ref>PMID:17144653</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Rhizobacterium japonicum kirchner 1896]] | + | [[Category: Bradyrhizobium japonicum]] |
| - | [[Category: Almo, S C]] | + | [[Category: Large Structures]] |
| - | [[Category: Fedorov, A A]] | + | [[Category: Almo SC]] |
| - | [[Category: Fedorov, E V]] | + | [[Category: Fedorov AA]] |
| - | [[Category: Gerlt, J A]] | + | [[Category: Fedorov EV]] |
| - | [[Category: Wood, B M]] | + | [[Category: Gerlt JA]] |
| - | [[Category: Yew, W S]] | + | [[Category: Wood BM]] |
| - | [[Category: D-tartrate dehydratase]] | + | [[Category: Yew WS]] |
| - | [[Category: Enolase superfamily]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Meso-tartrate]]
| + | |
| Structural highlights
Function
TARD_BRADU Catalyzes the dehydration of D-tartrate to oxaloacetate.[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
We focus on the assignment of function to and elucidation of structure-function relationships for a member of the mechanistically diverse enolase superfamily encoded by the Bradyrhizobium japonicum genome (bll6730; GI:27381841). As suggested by sequence alignments, the active site contains the same functional groups found in the active site of mandelate racemase (MR) that catalyzes a 1,1-proton transfer reaction: two acid/base catalysts, Lys 184 at the end of the second beta-strand, and a His 322-Asp 292 dyad at the ends of the seventh and sixth beta-strands, respectively, as well as ligands for an essential Mg2+, Asp 213, Glu 239, and Glu 265 at the ends of the third, fourth, and fifth beta-strands, respectively. We screened a library of 46 acid sugars and discovered that only d-tartrate is dehydrated, yielding oxaloacetate as product. The kinetic constants (kcat = 7.3 s(-1); kcat/KM = 8.5 x 10(4) M(-1) s(-1)) are consistent with assignment of the d-tartrate dehydratase (TarD) function. The kinetic phenotypes of mutants as well as the structures of liganded complexes are consistent with a mechanism in which Lys 184 initiates the reaction by abstraction of the alpha-proton to generate a Mg2+-stabilized enediolate intermediate, and the vinylogous beta-elimination of the 3-OH group is general acid-catalyzed by the His 322, accomplishing the anti-elimination of water. The replacement of the leaving group by solvent-derived hydrogen is stereorandom, suggesting that the enol tautomer of oxaloacetate is the product; this expectation was confirmed by its observation by 1H NMR spectroscopy. Thus, the TarD-catalyzed reaction is a "simple" extension of the two-step reaction catalyzed by MR: base-catalyzed proton abstraction to generate a Mg2+-stabilized enediolate intermediate followed by acid-catalyzed decomposition of that intermediate to yield the product.
Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum.,Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA Biochemistry. 2006 Dec 12;45(49):14598-608. PMID:17144653[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum. Biochemistry. 2006 Dec 12;45(49):14598-608. PMID:17144653 doi:10.1021/bi061688g
- ↑ Yew WS, Fedorov AA, Fedorov EV, Wood BM, Almo SC, Gerlt JA. Evolution of enzymatic activities in the enolase superfamily: D-tartrate dehydratase from Bradyrhizobium japonicum. Biochemistry. 2006 Dec 12;45(49):14598-608. PMID:17144653 doi:10.1021/bi061688g
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