2d2g

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[[Image:2d2g.gif|left|200px]]<br /><applet load="2d2g" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:2d2g.gif|left|200px]]
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caption="2d2g, resolution 1.85&Aring;" />
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'''OpdA from Agrobacterium radiobacter with bound product dimethylthiophosphate'''<br />
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{{Structure
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|PDB= 2d2g |SIZE=350|CAPTION= <scene name='initialview01'>2d2g</scene>, resolution 1.85&Aring;
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|SITE=
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|LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=CO2:CARBON+DIOXIDE'>CO2</scene> and <scene name='pdbligand=DZZ:O,O-DIMETHYL HYDROGEN THIOPHOSPHATE'>DZZ</scene>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1]
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|GENE=
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}}
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'''OpdA from Agrobacterium radiobacter with bound product dimethylthiophosphate'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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2D2G is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens] with <scene name='pdbligand=CO:'>CO</scene>, <scene name='pdbligand=CO2:'>CO2</scene> and <scene name='pdbligand=DZZ:'>DZZ</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Aryldialkylphosphatase Aryldialkylphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.8.1 3.1.8.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2G OCA].
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2D2G is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D2G OCA].
==Reference==
==Reference==
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The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism., Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL, Biochim Biophys Acta. 2005 Aug 31;1752(1):56-64. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16054447 16054447]
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The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism., Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL, Biochim Biophys Acta. 2005 Aug 31;1752(1):56-64. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16054447 16054447]
[[Category: Agrobacterium tumefaciens]]
[[Category: Agrobacterium tumefaciens]]
[[Category: Aryldialkylphosphatase]]
[[Category: Aryldialkylphosphatase]]
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[[Category: phosphotriesterase]]
[[Category: phosphotriesterase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:54:41 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:22:40 2008''

Revision as of 14:22, 20 March 2008

Image:2d2g.gif


PDB ID 2d2g

Drag the structure with the mouse to rotate
, resolution 1.85Å
Ligands: , and
Activity: Aryldialkylphosphatase, with EC number 3.1.8.1
Coordinates: save as pdb, mmCIF, xml



OpdA from Agrobacterium radiobacter with bound product dimethylthiophosphate


Overview

A detailed understanding of the catalytic mechanism of enzymes is an important step toward improving their activity for use in biotechnology. In this paper, crystal soaking experiments and X-ray crystallography were used to analyse the mechanism of the Agrobacterium radiobacter phosphotriesterase, OpdA, an enzyme capable of detoxifying a broad range of organophosphate pesticides. The structures of OpdA complexed with ethylene glycol and the product of dimethoate hydrolysis, dimethyl thiophosphate, provide new details of the catalytic mechanism. These structures suggest that the attacking nucleophile is a terminally bound hydroxide, consistent with the catalytic mechanism of other binuclear metallophosphoesterases. In addition, a crystal structure with the potential substrate trimethyl phosphate bound non-productively demonstrates the importance of the active site cavity in orienting the substrate into an approximation of the transition state.

About this Structure

2D2G is a Single protein structure of sequence from Agrobacterium tumefaciens. Full crystallographic information is available from OCA.

Reference

The structure of an enzyme-product complex reveals the critical role of a terminal hydroxide nucleophile in the bacterial phosphotriesterase mechanism., Jackson C, Kim HK, Carr PD, Liu JW, Ollis DL, Biochim Biophys Acta. 2005 Aug 31;1752(1):56-64. PMID:16054447

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