2w93

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:48, 13 December 2023) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:2w93.jpg|left|200px]]
 
-
<!--
+
==Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide==
-
The line below this paragraph, containing "STRUCTURE_2w93", creates the "Structure Box" on the page.
+
<StructureSection load='2w93' size='340' side='right'caption='[[2w93]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2w93]] is a 4 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=2W93 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W93 FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</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=PY0:(1S,2S)-1-AMINO-1,2-DIHYDROXYPROPAN-1-OLATE'>PY0</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-
{{STRUCTURE_2w93| PDB=2w93 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2w93 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w93 OCA], [https://pdbe.org/2w93 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w93 RCSB], [https://www.ebi.ac.uk/pdbsum/2w93 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w93 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/w9/2w93_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=2w93 ConSurf].
 +
<div style="clear:both"></div>
-
===CRYSTAL STRUCTURE OF THE SACCHAROMYCES CEREVISIAE PYRUVATE DECARBOXYLASE VARIANT E477Q IN COMPLEX WITH THE SURROGATE PYRUVAMIDE===
+
==See Also==
-
 
+
*[[Pyruvate decarboxylase|Pyruvate decarboxylase]]
-
 
+
== References ==
-
==About this Structure==
+
<references/>
-
2W93 is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W93 OCA].
+
__TOC__
-
[[Category: Pyruvate decarboxylase]]
+
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
-
[[Category: Konig, S.]]
+
[[Category: Konig S]]
-
[[Category: Kutter, S.]]
+
[[Category: Kutter S]]
-
[[Category: Weiss, M S.]]
+
[[Category: Weiss MS]]
-
[[Category: Acetylation]]
+
-
[[Category: Allosteric enzyme]]
+
-
[[Category: Branched-chain amino acid catabolism]]
+
-
[[Category: Cytoplasm]]
+
-
[[Category: Decarboxylase]]
+
-
[[Category: Lyase]]
+
-
[[Category: Magnesium]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Nucleus]]
+
-
[[Category: Phenylalanine catabolism]]
+
-
[[Category: Phosphoprotein]]
+
-
[[Category: Pyruvate decarboxylase]]
+
-
[[Category: Substrate activation]]
+
-
[[Category: Substrate regulation]]
+
-
[[Category: Thiamine pyrophosphate]]
+
-
[[Category: Thiohemiketal]]
+
-
[[Category: Tryptophan catabolism]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 4 11:21:01 2009''
+

Current revision

Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with the surrogate pyruvamide

PDB ID 2w93

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools