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2dw7

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{{STRUCTURE_2dw7| PDB=2dw7 | SCENE= }}
{{STRUCTURE_2dw7| PDB=2dw7 | SCENE= }}
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'''Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with Mg++ and meso-tartrate'''
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===Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with Mg++ and meso-tartrate===
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==Overview==
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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.
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==About this Structure==
==About this Structure==
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[[Category: Enolase superfamily]]
[[Category: Enolase superfamily]]
[[Category: Meso-tartrate]]
[[Category: Meso-tartrate]]
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Revision as of 18:17, 28 July 2008

Image:2dw7.png

Template:STRUCTURE 2dw7

Crystal structure of D-tartrate dehydratase from Bradyrhizobium japonicum complexed with Mg++ and meso-tartrate

Template:ABSTRACT PUBMED 17144653

About this Structure

2DW7 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

Page seeded by OCA on Mon Jul 28 21:17:26 2008

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