2q5o: Difference between revisions

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Revision as of 19:22, 20 March 2008

File:2q5o.jpg

, resolution 2.15Å

Ligands:

, , and

Gene:

ipdC (Azospirillum brasilense)

Activity:

Phenylpyruvate decarboxylase, with EC number 4.1.1.43

Coordinates:

save as pdb, mmCIF, xml

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 Thu Mar 20 18:22:00 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:2q5o.jpg|left|200px]]<br /><applet load="2q5o" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2q5o.jpg|left|200px]]
-caption="2q5o, resolution 2.15&Aring;" />
-'''X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate'''<br />
+ {{Structure
+|PDB= 2q5o |SIZE=350|CAPTION= <scene name='initialview01'>2q5o</scene>, resolution 2.15&Aring;
+|SITE=
+|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>
+|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]
+|GENE= ipdC ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192 Azospirillum brasilense])
+}}
+'''X-ray structure of phenylpyruvate decarboxylase in complex with 3-deaza-ThDP and phenylpyruvate'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-Q5O is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Azospirillum_brasilense Azospirillum brasilense] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=TPW:'>TPW</scene>, <scene name='pdbligand=PPY:'>PPY</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q5O OCA].
+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].
 ==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://ispc.weizmann.ac.il//pmbin/getpm?pmid=17905741 17905741]
+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]]
@@ Line 24: / Line 33: @@
 [[Category: PPY]]
 [[Category: TPW]]
-[[Category: closed active site loops]]
+[[Category: closed active site loop]]
 [[Category: lyase]]
 [[Category: substrate complex]]
-[[Category: symmetrical dimer of dimers]]
+[[Category: symmetrical dimer of dimer]]
 [[Category: thiamine diphosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:36:15 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:22:00 2008''