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| - | [[Image:1pyd.jpg|left|200px]]<br /><applet load="1pyd" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1pyd, resolution 2.4Å" /> | |
| - | '''CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION'''<br /> | |
| | | | |
| - | ==Overview== | + | ==CATALYTIC CENTERS IN THE THIAMIN DIPHOSPHATE DEPENDENT ENZYME PYRUVATE DECARBOXYLASE AT 2.4 ANGSTROMS RESOLUTION== |
| - | The crystal structure of brewers' yeast pyruvate decarboxylase, a thiamin, diphosphate dependent alpha-keto acid decarboxylase, has been determined, to 2.4-A resolution. The homotetrameric assembly contains two dimers, exhibiting strong intermonomer interactions within each dimer but more, limited ones between dimers. Each monomeric subunit is partitioned into, three structural domains, all folding according to a mixed alpha/beta, motif. Two of these domains are associated with cofactor binding, while, the other is associated with substrate activation. The catalytic centers, containing both thiamin diphosphate and Mg(II) are located deep in the, intermonomer interface within each dimer. Amino acids important in, cofactor binding and likely to participate in catalysis and substrate, activation are identified.
| + | <StructureSection load='1pyd' size='340' side='right'caption='[[1pyd]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1pyd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PYD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PYD FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></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=1pyd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pyd OCA], [https://pdbe.org/1pyd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pyd RCSB], [https://www.ebi.ac.uk/pdbsum/1pyd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pyd ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/PDC1_YEAST PDC1_YEAST] Major of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-ketoacids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins.<ref>PMID:4687392</ref> <ref>PMID:8866484</ref> <ref>PMID:9341119</ref> <ref>PMID:9748245</ref> <ref>PMID:10234824</ref> <ref>PMID:10231381</ref> <ref>PMID:10753893</ref> <ref>PMID:11141278</ref> <ref>PMID:12499363</ref> <ref>PMID:12902239</ref> |
| | + | == Evolutionary Conservation == |
| | + | [[Image:Consurf_key_small.gif|200px|right]] |
| | + | Check<jmol> |
| | + | <jmolCheckbox> |
| | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/py/1pyd_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | + | <text>to colour the structure by Evolutionary Conservation</text> |
| | + | </jmolCheckbox> |
| | + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pyd ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | ==About this Structure== | + | ==See Also== |
| - | 1PYD is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with MG and TDP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1PYD OCA].
| + | *[[Pyruvate decarboxylase|Pyruvate decarboxylase]] |
| - | | + | == References == |
| - | ==Reference== | + | <references/> |
| - | Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution., Dyda F, Furey W, Swaminathan S, Sax M, Farrenkopf B, Jordan F, Biochemistry. 1993 Jun 22;32(24):6165-70. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8512926 8512926]
| + | __TOC__ |
| - | [[Category: Pyruvate decarboxylase]] | + | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Saccharomyces cerevisiae]] | | [[Category: Saccharomyces cerevisiae]] |
| - | [[Category: Single protein]]
| + | [[Category: Dyda F]] |
| - | [[Category: Dyda, F.]] | + | [[Category: Furey W]] |
| - | [[Category: Furey, W.]] | + | |
| - | [[Category: MG]]
| + | |
| - | [[Category: TDP]]
| + | |
| - | [[Category: lyase(carbon-carbon)]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:13:51 2007''
| + | |
| Structural highlights
Function
PDC1_YEAST Major of three pyruvate decarboxylases (PDC1, PDC5, PDC6) implicated in the nonoxidative conversion of pyruvate to acetaldehyde and carbon dioxide during alcoholic fermentation. Most of the produced acetaldehyde is subsequently reduced to ethanol, but some is required for cytosolic acetyl-CoA production for biosynthetic pathways. The enzyme is also one of five 2-oxo acid decarboxylases (PDC1, PDC5, PDC6, ARO10, and THI3) able to decarboxylate more complex 2-oxo acids (alpha-ketoacids) than pyruvate, which seem mainly involved in amino acid catabolism. Here the enzyme catalyzes the decarboxylation of amino acids, which, in a first step, have been transaminated to the corresponding 2-oxo acids. In a third step, the resulting aldehydes are reduced to alcohols, collectively referred to as fusel oils or alcohols. Its preferred substrates are the transaminated amino acids valine, isoleucine, phenylalanine, and tryptophan, whereas leucine is no substrate. In a side-reaction the carbanionic intermediate (or active aldehyde) generated by decarboxylation or by activation of an aldehyde can react with an aldehyde via condensation (or carboligation) yielding a 2-hydroxy ketone, collectively called acyloins.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
See Also
References
- ↑ Lehmann H, Fischer G, Hubner G, Kohnert KD, Schellenberger A. The influence of steric and electronic parameters on the substrate behavior of -oxo acids to yeast pyruvate decarboxylase. Eur J Biochem. 1973 Jan 3;32(1):83-7. PMID:4687392
- ↑ Liesen T, Hollenberg CP, Heinisch JJ. ERA, a novel cis-acting element required for autoregulation and ethanol repression of PDC1 transcription in Saccharomyces cerevisiae. Mol Microbiol. 1996 Aug;21(3):621-32. PMID:8866484
- ↑ Dickinson JR, Lanterman MM, Danner DJ, Pearson BM, Sanz P, Harrison SJ, Hewlins MJ. A 13C nuclear magnetic resonance investigation of the metabolism of leucine to isoamyl alcohol in Saccharomyces cerevisiae. J Biol Chem. 1997 Oct 24;272(43):26871-8. PMID:9341119
- ↑ Dickinson JR, Harrison SJ, Hewlins MJ. An investigation of the metabolism of valine to isobutyl alcohol in Saccharomyces cerevisiae. J Biol Chem. 1998 Oct 2;273(40):25751-6. PMID:9748245
- ↑ Flikweert MT, de Swaaf M, van Dijken JP, Pronk JT. Growth requirements of pyruvate-decarboxylase-negative Saccharomyces cerevisiae. FEMS Microbiol Lett. 1999 May 1;174(1):73-9. PMID:10234824
- ↑ Eberhardt I, Cederberg H, Li H, Konig S, Jordan F, Hohmann S. Autoregulation of yeast pyruvate decarboxylase gene expression requires the enzyme but not its catalytic activity. Eur J Biochem. 1999 May;262(1):191-201. PMID:10231381
- ↑ Dickinson JR, Harrison SJ, Dickinson JA, Hewlins MJ. An investigation of the metabolism of isoleucine to active Amyl alcohol in Saccharomyces cerevisiae. J Biol Chem. 2000 Apr 14;275(15):10937-42. PMID:10753893
- ↑ Neuser F, Zorn H, Berger RG. Generation of odorous acyloins by yeast pyruvate decarboxylases and their occurrence in sherry and soy sauce. J Agric Food Chem. 2000 Dec;48(12):6191-5. PMID:11141278
- ↑ Dickinson JR, Salgado LE, Hewlins MJ. The catabolism of amino acids to long chain and complex alcohols in Saccharomyces cerevisiae. J Biol Chem. 2003 Mar 7;278(10):8028-34. Epub 2002 Dec 23. PMID:12499363 doi:10.1074/jbc.M211914200
- ↑ Vuralhan Z, Morais MA, Tai SL, Piper MD, Pronk JT. Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae. Appl Environ Microbiol. 2003 Aug;69(8):4534-41. PMID:12902239
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