2r1p

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:32, 3 April 2024) (edit) (undo)
 
(11 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2r1p.jpg|left|200px]]
 
-
<!--
+
==OpdA from Agrobacterium radiobacter with bound product diethyl thiophosphate from co-crystallisation with tetraethyl dithiopyrophosphate- 1.8 A==
-
The line below this paragraph, containing "STRUCTURE_2r1p", creates the "Structure Box" on the page.
+
<StructureSection load='2r1p' size='340' side='right'caption='[[2r1p]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2r1p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agrobacterium_tumefaciens Agrobacterium tumefaciens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R1P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R1P FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-
-->
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-
{{STRUCTURE_2r1p| PDB=2r1p | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r1p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r1p OCA], [https://pdbe.org/2r1p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r1p RCSB], [https://www.ebi.ac.uk/pdbsum/2r1p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r1p ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q93LD7_RHIRD Q93LD7_RHIRD]
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/r1/2r1p_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2r1p ConSurf].
 +
<div style="clear:both"></div>
-
'''OpdA from Agrobacterium radiobacter with bound product diethyl thiophosphate from co-crystallisation with tetraethyl dithiopyrophosphate- 1.8 A'''
+
==See Also==
-
 
+
*[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
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==
+
-
2R1P 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=2R1P 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:[http://www.ncbi.nlm.nih.gov/pubmed/18082180 18082180]
+
[[Category: Agrobacterium tumefaciens]]
[[Category: Agrobacterium tumefaciens]]
-
[[Category: Aryldialkylphosphatase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Carr PD]]
-
[[Category: Carr, P D.]]
+
[[Category: Foo JL]]
-
[[Category: Foo, J L.]]
+
[[Category: Jackson CJ]]
-
[[Category: Jackson, C J.]]
+
[[Category: Kim HK]]
-
[[Category: Kim, H K.]]
+
[[Category: Liu JW]]
-
[[Category: Liu, J W.]]
+
[[Category: Ollis DL]]
-
[[Category: Ollis, D L.]]
+
[[Category: Salem G]]
-
[[Category: Salem, G.]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Metalloenzyme]]
+
-
[[Category: Opda]]
+
-
[[Category: Phosphotriesterase]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 16:05:47 2008''
+

Current revision

OpdA from Agrobacterium radiobacter with bound product diethyl thiophosphate from co-crystallisation with tetraethyl dithiopyrophosphate- 1.8 A

PDB ID 2r1p

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2r1p"
Personal tools