2ji9: Difference between revisions

← Older edit Newer edit →

Revision as of 18:42, 20 March 2008

File:2ji9.jpg

, resolution 2.20Å

Sites:

Ligands:

, , and

Activity:

Oxalyl-CoA decarboxylase, with EC number 4.1.1.8

Coordinates:

save as pdb, mmCIF, xml

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 Thu Mar 20 17:42:15 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]]<br /><applet load="2ji9" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2ji9.jpg|left|200px]]
-caption="2ji9, resolution 2.20&Aring;" />
-'''X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP'''<br />
+ {{Structure
+|PDB= 2ji9 |SIZE=350|CAPTION= <scene name='initialview01'>2ji9</scene>, resolution 2.20&Aring;
+|SITE= <scene name='pdbsite=AC1:B3p+Binding+Site+For+Chain+B'>AC1</scene>
+|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=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>
+|ACTIVITY= [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]
+|GENE=
+}}
+'''X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH 3-DEAZA-THDP'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-JI9 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Oxalobacter_formigenes Oxalobacter formigenes] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=TPW:'>TPW</scene>, <scene name='pdbligand=ADP:'>ADP</scene> and <scene name='pdbligand=B3P:'>B3P</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Site: <scene name='pdbsite=AC1:B3p+Binding+Site+For+Chain+B'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI9 OCA].
+JI9 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Oxalobacter_formigenes Oxalobacter formigenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JI9 OCA].
 ==Reference==
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17637344 17637344]
+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:[http://www.ncbi.nlm.nih.gov/pubmed/17637344 17637344]
 [[Category: Oxalobacter formigenes]]
 [[Category: Oxalyl-CoA decarboxylase]]
@@ Line 34: / Line 43: @@
 [[Category: thiamine pyrophosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:03:35 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:42:15 2008''