2ji9: Difference between revisions

Revision as of 08:57, 4 May 2008

X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP

OverviewOverview

Despite more than five decades of extensive studies of thiamin diphosphate (ThDP) enzymes, there remain many uncertainties as to how these enzymes achieve their rate enhancements. Here, we present a clear picture of catalysis for the simple nonoxidative decarboxylase, oxalyl-coenzyme A (CoA) decarboxylase, based on crystallographic snapshots along the catalytic cycle and kinetic data on active site mutants. First, we provide crystallographic evidence that, upon binding of oxalyl-CoA, the C-terminal 13 residues fold over the substrate, aligning the substrate alpha-carbon for attack by the ThDP-C2 atom. The second structure presented shows a covalent reaction intermediate after decarboxylation, interpreted as being nonplanar. Finally, the structure of a product complex is presented. In accordance with mutagenesis data, no side chains of the enzyme are implied to directly participate in proton transfer except the glutamic acid (Glu-56), which promotes formation of the 1',4'-iminopyrimidine tautomer of ThDP needed for activation.

About this StructureAbout this Structure

2JI9 is a Single protein structure of sequence from Oxalobacter formigenes. Full crystallographic information is available from OCA.

ReferenceReference

Crystallographic snapshots of oxalyl-CoA decarboxylase give insights into catalysis by nonoxidative ThDP-dependent decarboxylases., Berthold CL, Toyota CG, Moussatche P, Wood MD, Leeper F, Richards NG, Lindqvist Y, Structure. 2007 Jul;15(7):853-61. PMID:17637344 Page seeded by OCA on Sun May 4 08:57:24 2008

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

OCA

@@ Line 1: / Line 1: @@
 [[Image:2ji9.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 2ji9 |SIZE=350|CAPTION= <scene name='initialview01'>2ji9</scene>, resolution 2.20&Aring;
+The line below this paragraph, containing "STRUCTURE_2ji9", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:B3p+Binding+Site+For+Chain+B'>AC1</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <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>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxalyl-CoA_decarboxylase Oxalyl-CoA decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.8 4.1.1.8] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE=
+-->
-|DOMAIN=
+{{STRUCTURE_2ji9|  PDB=2ji9  |  SCENE=  }}
-|RELATEDENTRY=[[2c31|2C31]], [[2ji6|2JI6]], [[2ji7|2JI7]], [[2ji8|2JI8]], [[2jib|2JIB]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ji9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ji9 OCA], [http://www.ebi.ac.uk/pdbsum/2ji9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ji9 RCSB]</span>
-}}
 '''X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP'''
@@ Line 33: / Line 30: @@
 [[Category: Toyota, C G.]]
 [[Category: Wood, M D.]]
-[[Category: cofactor analogue inhibitor complex]]
+[[Category: Cofactor analogue inhibitor complex]]
-[[Category: decarboxylase]]
+[[Category: Decarboxylase]]
-[[Category: flavoprotein]]
+[[Category: Flavoprotein]]
-[[Category: lyase]]
+[[Category: Lyase]]
-[[Category: non- oxidative decarboxylase]]
+[[Category: Non- oxidative decarboxylase]]
-[[Category: oxalate degradation]]
+[[Category: Oxalate degradation]]
-[[Category: thiamin diphosphate-dependent]]
+[[Category: Thiamin diphosphate-dependent]]
-[[Category: thiamine pyrophosphate]]
+[[Category: Thiamine pyrophosphate]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 08:57:24 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 03:58:35 2008''