2q5o: Difference between revisions

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-[[Image:2q5o.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2q5o", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2q5o|  PDB=2q5o  |  SCENE=  }}
-'''X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate'''
+==X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate==
+<StructureSection load='2q5o' size='340' side='right'caption='[[2q5o]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+== Structural highlights ==
+<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>
+</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>
+<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.
-==Overview==
+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>
-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.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-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].
+</div>
+<div class="pdbe-citations 2q5o" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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]
+*[[Phenylpyruvate decarboxylase|Phenylpyruvate decarboxylase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[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: 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 Sun May  4 14:24:09 2008''