2q5o: Difference between revisions

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-[[Image:2q5o.jpg|left|200px]]
- {{Structure
+==X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate==
-|PDB= 2q5o |SIZE=350|CAPTION= <scene name='initialview01'>2q5o</scene>, resolution 2.15&Aring;
+<StructureSection load='2q5o' size='340' side='right'caption='[[2q5o]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPW:2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TPW</scene>, <scene name='pdbligand=PPY:3-PHENYLPYRUVIC+ACID'>PPY</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+<table><tr><td colspan='2'>[[2q5o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Azospirillum_brasilense Azospirillum brasilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q5O FirstGlance]. <br>
-|ACTIVITY= [http://en.wikipedia.org/wiki/Phenylpyruvate_decarboxylase Phenylpyruvate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.43 4.1.1.43]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
-|GENE= ipdC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192 Azospirillum brasilense])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PPY:3-PHENYLPYRUVIC+ACID'>PPY</scene>, <scene name='pdbligand=TPW:2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TPW</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=2q5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q5o OCA], [https://pdbe.org/2q5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q5o RCSB], [https://www.ebi.ac.uk/pdbsum/2q5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q5o ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DCIP_AZOBR DCIP_AZOBR]
+== 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/q5/2q5o_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=2q5o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.
-'''X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate'''
+Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase.,Versees W, Spaepen S, Wood MD, Leeper FJ, Vanderleyden J, Steyaert J J Biol Chem. 2007 Nov 30;282(48):35269-78. Epub 2007 Sep 28. PMID:17905741<ref>PMID:17905741</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2q5o" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Thiamine diphosphate-dependent enzymes are involved in a wide variety of metabolic pathways. The molecular mechanism behind active site communication and substrate activation, observed in some of these enzymes, has since long been an area of debate. Here, we report the crystal structures of a phenylpyruvate decarboxylase in complex with its substrates and a covalent reaction intermediate analogue. These structures reveal the regulatory site and unveil the mechanism of allosteric substrate activation. This signal transduction relies on quaternary structure reorganizations, domain rotations, and a pathway of local conformational changes that are relayed from the regulatory site to the active site. The current findings thus uncover the molecular mechanism by which the binding of a substrate in the regulatory site is linked to the mounting of the catalytic machinery in the active site in this thiamine diphosphate-dependent enzyme.
+*[[Phenylpyruvate decarboxylase|Phenylpyruvate decarboxylase]]
+== References ==
-==About this Structure==
+<references/>
-Q5O is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Azospirillum_brasilense Azospirillum brasilense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q5O OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Molecular mechanism of allosteric substrate activation in a thiamine diphosphate-dependent decarboxylase., Versees W, Spaepen S, Wood MD, Leeper FJ, Vanderleyden J, Steyaert J, J Biol Chem. 2007 Nov 30;282(48):35269-78. Epub 2007 Sep 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17905741 17905741]
 [[Category: Azospirillum brasilense]]
-[[Category: Phenylpyruvate decarboxylase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Leeper FJ]]
-[[Category: Leeper, F J.]]
+[[Category: Spaepen S]]
-[[Category: Spaepen, S.]]
+[[Category: Steyaert J]]
-[[Category: Steyaert, J.]]
+[[Category: Vanderleyden J]]
-[[Category: Vanderleyden, J.]]
+[[Category: Versees W]]
-[[Category: Versees, W.]]
+[[Category: Wood MD]]
-[[Category: Wood, M D.]]
-[[Category: GOL]]
-[[Category: MG]]
-[[Category: PPY]]
-[[Category: TPW]]
-[[Category: closed active site loop]]
-[[Category: lyase]]
-[[Category: substrate complex]]
-[[Category: symmetrical dimer of dimer]]
-[[Category: thiamine diphosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:22:00 2008''