3a3w: Difference between revisions
New page: '''Unreleased structure''' The entry 3a3w is ON HOLD until Paper Publication Authors: Ollis, D.L., Tawfik, D.S., Schenk, G., Jackson, C.J., Foo, J.L., Tokuriki, N., Afriat, L., Carr, P.... |
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==Structure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/I260T/G273S) with diethyl 4-methoxyphenyl phosphate bound in the active site== | |||
<StructureSection load='3a3w' size='340' side='right'caption='[[3a3w]], [[Resolution|resolution]] 1.85Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3a3w]] 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=3A3W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A3W FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85Å</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=EPL:DIETHYL+4-METHOXYPHENYL+PHOSPHATE'>EPL</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a3w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a3w OCA], [https://pdbe.org/3a3w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a3w RCSB], [https://www.ebi.ac.uk/pdbsum/3a3w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a3w 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/a3/3a3w_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=3a3w ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
To efficiently catalyze a chemical reaction, enzymes are required to maintain fast rates for formation of the Michaelis complex, the chemical reaction and product release. These distinct demands could be satisfied via fluctuation between different conformational substates (CSs) with unique configurations and catalytic properties. However, there is debate as to how these rapid conformational changes, or dynamics, exactly affect catalysis. As a model system, we have studied bacterial phosphotriesterase (PTE), which catalyzes the hydrolysis of the pesticide paraoxon at rates limited by a physical barrier-either substrate diffusion or conformational change. The mechanism of paraoxon hydrolysis is understood in detail and is based on a single, dominant, enzyme conformation. However, the other aspects of substrate turnover (substrate binding and product release), although possibly rate-limiting, have received relatively little attention. This work identifies "open" and "closed" CSs in PTE and dominant structural transition in the enzyme that links them. The closed state is optimally preorganized for paraoxon hydrolysis, but seems to block access to/from the active site. In contrast, the open CS enables access to the active site but is poorly organized for hydrolysis. Analysis of the structural and kinetic effects of mutations distant from the active site suggests that remote mutations affect the turnover rate by altering the conformational landscape. | |||
Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase.,Jackson CJ, Foo JL, Tokuriki N, Afriat L, Carr PD, Kim HK, Schenk G, Tawfik DS, Ollis DL Proc Natl Acad Sci U S A. 2009 Dec 4. PMID:19966226<ref>PMID:19966226</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3a3w" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Phosphotriesterase 3D structures|Phosphotriesterase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Agrobacterium tumefaciens]] | |||
[[Category: Large Structures]] | |||
[[Category: Afriat L]] | |||
[[Category: Carr PD]] | |||
[[Category: Foo JL]] | |||
[[Category: Jackson CJ]] | |||
[[Category: Kim HK]] | |||
[[Category: Ollis DL]] | |||
[[Category: Schenk G]] | |||
[[Category: Tawfik DS]] | |||
[[Category: Tokuriki N]] | |||
Latest revision as of 17:09, 1 November 2023
Structure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/I260T/G273S) with diethyl 4-methoxyphenyl phosphate bound in the active siteStructure of OpdA mutant (G60A/A80V/S92A/R118Q/K185R/Q206P/D208G/I260T/G273S) with diethyl 4-methoxyphenyl phosphate bound in the active site
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedTo efficiently catalyze a chemical reaction, enzymes are required to maintain fast rates for formation of the Michaelis complex, the chemical reaction and product release. These distinct demands could be satisfied via fluctuation between different conformational substates (CSs) with unique configurations and catalytic properties. However, there is debate as to how these rapid conformational changes, or dynamics, exactly affect catalysis. As a model system, we have studied bacterial phosphotriesterase (PTE), which catalyzes the hydrolysis of the pesticide paraoxon at rates limited by a physical barrier-either substrate diffusion or conformational change. The mechanism of paraoxon hydrolysis is understood in detail and is based on a single, dominant, enzyme conformation. However, the other aspects of substrate turnover (substrate binding and product release), although possibly rate-limiting, have received relatively little attention. This work identifies "open" and "closed" CSs in PTE and dominant structural transition in the enzyme that links them. The closed state is optimally preorganized for paraoxon hydrolysis, but seems to block access to/from the active site. In contrast, the open CS enables access to the active site but is poorly organized for hydrolysis. Analysis of the structural and kinetic effects of mutations distant from the active site suggests that remote mutations affect the turnover rate by altering the conformational landscape. Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase.,Jackson CJ, Foo JL, Tokuriki N, Afriat L, Carr PD, Kim HK, Schenk G, Tawfik DS, Ollis DL Proc Natl Acad Sci U S A. 2009 Dec 4. PMID:19966226[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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