2c3p: Difference between revisions

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Revision as of 17:10, 20 March 2008

File:2c3p.gif

, resolution 2.33Å

Sites:

Ligands:

, , and

Activity:

Pyruvate synthase, with EC number 1.2.7.1

Coordinates:

save as pdb, mmCIF, xml

CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS

OverviewOverview

Pyruvate-ferredoxin oxidoreductases (PFOR) are unique among thiamine pyrophosphate (ThDP)-containing enzymes in giving rise to a rather stable cofactor-based free-radical species upon the decarboxylation of their first substrate, pyruvate. We have obtained snapshots of unreacted and partially reacted (probably as a tetrahedral intermediate) pyruvate-PFOR complexes at different time intervals. We conclude that pyruvate decarboxylation involves very limited substrate-to-product movements but a significant displacement of the thiazolium moiety of ThDP. In this respect, PFOR seems to differ substantially from other ThDP-containing enzymes, such as transketolase and pyruvate decarboxylase. In addition, exposure of PFOR to oxygen in the presence of pyruvate results in significant inhibition of catalytic activity, both in solution and in the crystals. Examination of the crystal structure of inhibited PFOR suggests that the loss of activity results from oxime formation at the 4' amino substituent of the pyrimidine moiety of ThDP.

About this StructureAbout this Structure

2C3P is a Single protein structure of sequence from Desulfovibrio africanus. Full crystallographic information is available from OCA.

ReferenceReference

Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate., Cavazza C, Contreras-Martel C, Pieulle L, Chabriere E, Hatchikian EC, Fontecilla-Camps JC, Structure. 2006 Feb;14(2):217-24. PMID:16472741

Page seeded by OCA on Thu Mar 20 16:10:22 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2c3p.gif|left|200px]]<br /><applet load="2c3p" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2c3p.gif|left|200px]]
-caption="2c3p, resolution 2.33&Aring;" />
-'''CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS'''<br />
+ {{Structure
+|PDB= 2c3p |SIZE=350|CAPTION= <scene name='initialview01'>2c3p</scene>, resolution 2.33&Aring;
+|SITE= <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+B'>AC1</scene>
+|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene> and <scene name='pdbligand=1TP:1-(2-{(2S,4R,5R)-3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-[(1S)-1-CARBOXY-1-HYDROXYETHYL]-4-METHYL-1,3-THIAZOLIDIN-5-YL}ETHOXY)-1,1,3,3-TETRAHYDROXY-1LAMBDA~5~-DIPHOSPHOX-1-EN-2-IUM 3-OXIDE'>1TP</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Pyruvate_synthase Pyruvate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.7.1 1.2.7.1]
+|GENE=
+}}
+'''CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM DESULFOVIBRIO AFRICANUS'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-C3P is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=CA:'>CA</scene>, <scene name='pdbligand=SF4:'>SF4</scene> and <scene name='pdbligand=1TP:'>1TP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Pyruvate_synthase Pyruvate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.7.1 1.2.7.1] Known structural/functional Site: <scene name='pdbsite=AC1:Ca+Binding+Site+For+Chain+B'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C3P OCA].
+C3P is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_africanus Desulfovibrio africanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C3P OCA].
 ==Reference==
-Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate., Cavazza C, Contreras-Martel C, Pieulle L, Chabriere E, Hatchikian EC, Fontecilla-Camps JC, Structure. 2006 Feb;14(2):217-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16472741 16472741]
+Flexibility of thiamine diphosphate revealed by kinetic crystallographic studies of the reaction of pyruvate-ferredoxin oxidoreductase with pyruvate., Cavazza C, Contreras-Martel C, Pieulle L, Chabriere E, Hatchikian EC, Fontecilla-Camps JC, Structure. 2006 Feb;14(2):217-24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16472741 16472741]
 [[Category: Desulfovibrio africanus]]
 [[Category: Pyruvate synthase]]
@@ Line 24: / Line 33: @@
 [[Category: MG]]
 [[Category: SF4]]
-[[Category: 4fe-4s]]
+[[Category: 4fe-4]]
 [[Category: electron transport]]
 [[Category: iron]]
@@ Line 34: / Line 43: @@
 [[Category: tpp-dependent enzyme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:44:33 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:10:22 2008''