4jd5: Difference between revisions
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==Crystal Structure of Benzoylformate Decarboxylase Mutant L403E== | |||
=== | <StructureSection load='4jd5' size='340' side='right' caption='[[4jd5]], [[Resolution|resolution]] 1.33Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4jd5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JD5 FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=TZD:2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TZD</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gpe|4gpe]], [[4gm4|4gm4]], [[4gg1|4gg1]], [[4gm1|4gm1]], [[4gm0|4gm0]], [[4gp9|4gp9]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">mdlC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=303 Pseudomonas putida])</td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Benzoylformate_decarboxylase Benzoylformate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.7 4.1.1.7] </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=4jd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jd5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jd5 RCSB], [http://www.ebi.ac.uk/pdbsum/4jd5 PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
It is widely accepted that, in thiamin diphosphate (ThDP)-dependent enzymes, much of the rate acceleration is provided by the cofactor. Inter alia, the reactive conformation of ThDP, known as the V-conformation, has been attributed to the presence of a bulky hydrophobic residue located directly below the cofactor. Here we report the use of site-saturation mutagenesis to generate variants of this residue (Leu403) in benzoylformate decarboxylase. The observed 3 orders of magnitude range in kcat/Km values suggested that conformational changes in the cofactor could be influencing catalysis. However, X-ray structures of several variants were determined, and there was remarkably little change in ThDP conformation. Rather, it seemed that, once the V-conformation was attained, residue size and hydrophobicity were more important for enzyme activity. | |||
A bulky hydrophobic residue is not required to maintain the v-conformation of enzyme-bound thiamin diphosphate.,Andrews FH, Tom AR, Gunderman PR, Novak WR, McLeish MJ Biochemistry. 2013 May 7;52(18):3028-30. doi: 10.1021/bi400368j. Epub 2013 Apr, 23. PMID:23607689<ref>PMID:23607689</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Benzoylformate decarboxylase]] | [[Category: Benzoylformate decarboxylase]] | ||
[[Category: Pseudomonas putida]] | [[Category: Pseudomonas putida]] | ||
[[Category: Andrews, F H | [[Category: Andrews, F H]] | ||
[[Category: Gunderman, P R | [[Category: Gunderman, P R]] | ||
[[Category: McLeish, M J | [[Category: McLeish, M J]] | ||
[[Category: Novak, W R.P | [[Category: Novak, W R.P]] | ||
[[Category: Tom, A R | [[Category: Tom, A R]] | ||
[[Category: Decarboxylase]] | [[Category: Decarboxylase]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Thiamin thiazolone diphosphate cofactor]] | [[Category: Thiamin thiazolone diphosphate cofactor]] | ||
Revision as of 14:45, 5 January 2015
Crystal Structure of Benzoylformate Decarboxylase Mutant L403E
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