This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
4gpe
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | + | ==Crystal Structure of Benzoylformate Decarboxylase Mutant L403M== | |
| - | + | <StructureSection load='4gpe' size='340' side='right' caption='[[4gpe]], [[Resolution|resolution]] 1.39Å' scene=''> | |
| - | { | + | == Structural highlights == |
| + | <table><tr><td colspan='2'>[[4gpe]] 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=4GPE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GPE 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">[[4gg1|4gg1]], [[4gm0|4gm0]], [[4gm1|4gm1]], [[4gm4|4gm4]], [[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=4gpe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gpe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gpe RCSB], [http://www.ebi.ac.uk/pdbsum/4gpe 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 14:59, 5 January 2015
Crystal Structure of Benzoylformate Decarboxylase Mutant L403M
| |||||||||||
