2dw6
From Proteopedia
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|PDB= 2dw6 |SIZE=350|CAPTION= <scene name='initialview01'>2dw6</scene>, resolution 2.30Å | |PDB= 2dw6 |SIZE=350|CAPTION= <scene name='initialview01'>2dw6</scene>, resolution 2.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene> |
| - | |ACTIVITY= [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] | + | |ACTIVITY= <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> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1tzz|1TZZ]], [[2dw7|2DW7]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dw6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dw6 OCA], [http://www.ebi.ac.uk/pdbsum/2dw6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dw6 RCSB]</span> | ||
}} | }} | ||
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[[Category: Wood, B M.]] | [[Category: Wood, B M.]] | ||
[[Category: Yew, W S.]] | [[Category: Yew, W S.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: TAR]] | ||
| - | [[Category: TLA]] | ||
[[Category: d-tartrate]] | [[Category: d-tartrate]] | ||
[[Category: d-tartrate dehydratase]] | [[Category: d-tartrate dehydratase]] | ||
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[[Category: l-tartrate]] | [[Category: l-tartrate]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:40:30 2008'' |
Revision as of 23:40, 30 March 2008
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| , resolution 2.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Activity: | D(-)-tartrate dehydratase, with EC number 4.2.1.81 | ||||||
| Related: | 1TZZ, 2DW7
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate
Overview
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.
About this Structure
2DW6 is a Single protein structure of sequence from Bradyrhizobium japonicum. Full crystallographic information is available from OCA.
Reference
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
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