3c86

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[[Image:3c86.jpg|left|200px]]
[[Image:3c86.jpg|left|200px]]
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{{Structure
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<!--
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|PDB= 3c86 |SIZE=350|CAPTION= <scene name='initialview01'>3c86</scene>, resolution 1.80&Aring;
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The line below this paragraph, containing "STRUCTURE_3c86", creates the "Structure Box" on the page.
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|SITE= <scene name='pdbsite=AC1:Fe2+Binding+Site+For+Residue+A+800'>AC1</scene>, <scene name='pdbsite=AC2:Co+Binding+Site+For+Residue+A+801'>AC2</scene>, <scene name='pdbsite=AC3:Dpj+Binding+Site+For+Residue+A+1'>AC3</scene> and <scene name='pdbsite=AC4:Edo+Binding+Site+For+Residue+A+701'>AC4</scene>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=DPJ:O,O-DIETHYL+HYDROGEN+THIOPHOSPHATE'>DPJ</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=LCX:CARBOXYLATED+LYSINE'>LCX</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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or leave the SCENE parameter empty for the default display.
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|GENE= opdA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=358 Agrobacterium tumefaciens])
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-->
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|DOMAIN=
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{{STRUCTURE_3c86| PDB=3c86 | SCENE= }}
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|RELATEDENTRY=[[2d2j|2D2J]], [[2d2h|2D2H]], [[2d2g|2D2G]], [[2r1k|2R1K]], [[2r1l|2R1L]], [[2r1m|2R1M]], [[2r1n|2R1N]], [[2r1p|2R1P]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3c86 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c86 OCA], [http://www.ebi.ac.uk/pdbsum/3c86 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3c86 RCSB]</span>
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}}
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'''OpdA from agrobacterium radiobacter with bound product diethyl thiophosphate from crystal soaking with tetraethyl dithiopyrophosphate- 1.8 A'''
'''OpdA from agrobacterium radiobacter with bound product diethyl thiophosphate from crystal soaking with tetraethyl dithiopyrophosphate- 1.8 A'''
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==About this Structure==
==About this Structure==
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3C86 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. This structure supersedes the now removed PDB entry 2R1O. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C86 OCA].
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3C86 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2r1o 2r1o]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C86 OCA].
==Reference==
==Reference==
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[[Category: Ollis, D L.]]
[[Category: Ollis, D L.]]
[[Category: Salem, G.]]
[[Category: Salem, G.]]
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[[Category: hydrolase]]
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[[Category: Hydrolase]]
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[[Category: metalloenzyme]]
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[[Category: Metalloenzyme]]
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[[Category: opda]]
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[[Category: Opda]]
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[[Category: phosphotriesterase]]
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[[Category: Phosphotriesterase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 21:26:10 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:31:02 2008''
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Revision as of 18:26, 4 May 2008

Image:3c86.jpg

Template:STRUCTURE 3c86

OpdA from agrobacterium radiobacter with bound product diethyl thiophosphate from crystal soaking with tetraethyl dithiopyrophosphate- 1.8 A


Overview

The mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The mu-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems has indicated that mu-hydroxo bridges are often not themselves nucleophiles, but act as general bases for freely exchangeable nucleophilic water molecules. Herein, we present crystallographic analyses of a bacterial PTE from Agrobacterium radiobacter, OpdA, capturing the enzyme-substrate complex during hydrolysis. This model of the Michaelis complex suggests the alignment of the substrate will favour attack from a solvent molecule terminally coordinated to the alpha-metal ion. The bridging of both metal ions by the product, without disruption of the mu-hydroxo bridge, is also consistent with nucleophilic attack occurring from the terminal position. When phosphodiesters are soaked into crystals of OpdA, they coordinate bidentately to the beta-metal ion, displacing the mu-hydroxo bridge. Thus, alternative product-binding modes exist for the PTEs, and it is the bridging mode that appears to result from phosphotriester hydrolysis. Kinetic analysis of the PTE and promiscuous phosphodiesterase activities confirms that the presence of a mu-hydroxo bridge during phosphotriester hydrolysis is correlated with a lower pK(a) for the nucleophile, consistent with a general base function during catalysis.

About this Structure

3C86 is a Single protein structure of sequence from Agrobacterium tumefaciens. This structure supersedes the now removed PDB entry 2r1o. Full crystallographic information is available from OCA.

Reference

In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase., Jackson CJ, Foo JL, Kim HK, Carr PD, Liu JW, Salem G, Ollis DL, J Mol Biol. 2008 Feb 1;375(5):1189-96. Epub 2007 Nov 1. PMID:18082180 Page seeded by OCA on Sun May 4 21:26:10 2008

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