2q5o: Difference between revisions

Revision as of 14:24, 4 May 2008

X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate

OverviewOverview

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 StructureAbout this Structure

2Q5O is a Single protein structure of sequence from Azospirillum brasilense. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Sun May 4 14:24:09 2008

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OCA

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 [[Image:2q5o.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2q5o |SIZE=350|CAPTION= <scene name='initialview01'>2q5o</scene>, resolution 2.15&Aring;
+The line below this paragraph, containing "STRUCTURE_2q5o", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <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>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[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] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= ipdC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192 Azospirillum brasilense])
+-->
-|DOMAIN=
+{{STRUCTURE_2q5o|  PDB=2q5o  |  SCENE=  }}
-|RELATEDENTRY=[[2nxw|2nxw]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2q5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q5o OCA], [http://www.ebi.ac.uk/pdbsum/2q5o PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2q5o RCSB]</span>
-}}
 '''X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate'''
@@ Line 32: / Line 29: @@
 [[Category: Versees, W.]]
 [[Category: Wood, M D.]]
-[[Category: closed active site loop]]
+[[Category: Closed active site loop]]
-[[Category: lyase]]
+[[Category: Lyase]]
-[[Category: substrate complex]]
+[[Category: Substrate complex]]
-[[Category: symmetrical dimer of dimer]]
+[[Category: Symmetrical dimer of dimer]]
-[[Category: thiamine diphosphate]]
+[[Category: Thiamine diphosphate]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:24:09 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:45:05 2008''