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| | <StructureSection load='5euj' size='340' side='right'caption='[[5euj]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='5euj' size='340' side='right'caption='[[5euj]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5euj]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_51623 Atcc 51623]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5EUJ FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5euj]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Zymobacter_palmae Zymobacter palmae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EUJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EUJ FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pdc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=33074 ATCC 51623])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5euj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euj OCA], [https://pdbe.org/5euj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5euj RCSB], [https://www.ebi.ac.uk/pdbsum/5euj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5euj ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5euj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5euj OCA], [http://pdbe.org/5euj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5euj RCSB], [http://www.ebi.ac.uk/pdbsum/5euj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5euj ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q8KTX6_9GAMM Q8KTX6_9GAMM] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 51623]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyruvate decarboxylase]] | + | [[Category: Zymobacter palmae]] |
| - | [[Category: Andrews, E S.V]] | + | [[Category: Andrews ESV]] |
| - | [[Category: Arcus, V L]] | + | [[Category: Arcus VL]] |
| - | [[Category: Buddrus, L]] | + | [[Category: Buddrus L]] |
| - | [[Category: Crennell, S J]] | + | [[Category: Crennell SJ]] |
| - | [[Category: Danson, M J]] | + | [[Category: Danson MJ]] |
| - | [[Category: Leak, D J]] | + | [[Category: Leak DJ]] |
| - | [[Category: Lyase]]
| + | |
| Structural highlights
Function
Q8KTX6_9GAMM
Publication Abstract from PubMed
Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg(2+) ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 A resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 A and Rr.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were Rwork = 0.186 (0.271 in the highest resolution bin) and Rfree = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions.
Crystal structure of pyruvate decarboxylase from Zymobacter palmae.,Buddrus L, Andrews ES, Leak DJ, Danson MJ, Arcus VL, Crennell SJ Acta Crystallogr F Struct Biol Commun. 2016 Sep;72(Pt 9):700-6. doi:, 10.1107/S2053230X16012012. Epub 2016 Aug 26. PMID:27599861[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Buddrus L, Andrews ES, Leak DJ, Danson MJ, Arcus VL, Crennell SJ. Crystal structure of pyruvate decarboxylase from Zymobacter palmae. Acta Crystallogr F Struct Biol Commun. 2016 Sep;72(Pt 9):700-6. doi:, 10.1107/S2053230X16012012. Epub 2016 Aug 26. PMID:27599861 doi:http://dx.doi.org/10.1107/S2053230X16012012
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