2jib

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[[Image:2jib.jpg|left|200px]]<br /><applet load="2jib" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2jib.jpg|left|200px]]
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caption="2jib, resolution 2.20&Aring;" />
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'''X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH COENZYME-A'''<br />
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{{Structure
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|PDB= 2jib |SIZE=350|CAPTION= <scene name='initialview01'>2jib</scene>, resolution 2.20&Aring;
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|SITE= <scene name='pdbsite=AC1:Pge+Binding+Site+For+Chain+B'>AC1</scene>
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|LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene>, <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=PGE:TRIETHYLENE GLYCOL'>PGE</scene>
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|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]
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|GENE=
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}}
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'''X-RAY STRUCTURE OF OXALYL-COA DECARBOXYLASE IN COMPLEX WITH COENZYME-A'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2JIB 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=COA:'>COA</scene>, <scene name='pdbligand=TPP:'>TPP</scene>, <scene name='pdbligand=ADP:'>ADP</scene> and <scene name='pdbligand=PGE:'>PGE</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:Pge+Binding+Site+For+Chain+B'>AC1</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JIB OCA].
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2JIB 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=2JIB OCA].
==Reference==
==Reference==
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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]
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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: Oxalobacter formigenes]]
[[Category: Oxalyl-CoA decarboxylase]]
[[Category: Oxalyl-CoA decarboxylase]]
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[[Category: thiamine pyrophosphate]]
[[Category: thiamine pyrophosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:03:35 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:42:18 2008''

Revision as of 15:42, 20 March 2008

Image:2jib.jpg


PDB ID 2jib

Drag the structure with the mouse to rotate
, 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 COENZYME-A


Overview

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 Structure

2JIB is a Single protein structure of sequence from Oxalobacter formigenes. Full crystallographic information is available from 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:17637344

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