2dw6

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[[Image:2dw6.jpg|left|200px]]<br /><applet load="2dw6" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2dw6.jpg|left|200px]]
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caption="2dw6, resolution 2.30&Aring;" />
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'''Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate'''<br />
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{{Structure
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|PDB= 2dw6 |SIZE=350|CAPTION= <scene name='initialview01'>2dw6</scene>, resolution 2.30&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=TLA:L(+)-TARTARIC ACID'>TLA</scene>
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|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]
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|GENE=
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}}
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'''Crystal structure of the mutant K184A of D-Tartrate Dehydratase from Bradyrhizobium japonicum complexed with Mg++ and D-tartrate'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2DW6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum] with <scene name='pdbligand=TAR:'>TAR</scene>, <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=TLA:'>TLA</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA].
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2DW6 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bradyrhizobium_japonicum Bradyrhizobium japonicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DW6 OCA].
==Reference==
==Reference==
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17144653 17144653]
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17144653 17144653]
[[Category: Bradyrhizobium japonicum]]
[[Category: Bradyrhizobium japonicum]]
[[Category: D(-)-tartrate dehydratase]]
[[Category: D(-)-tartrate dehydratase]]
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[[Category: l-tartrate]]
[[Category: l-tartrate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 17:03:20 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:32:21 2008''

Revision as of 14:32, 20 March 2008


PDB ID 2dw6

Drag the structure with the mouse to rotate
, resolution 2.30Å
Ligands: , and
Activity: D(-)-tartrate dehydratase, with EC number 4.2.1.81
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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