3fcj: Difference between revisions
New page: '''Unreleased structure''' The entry 3fcj is ON HOLD Authors: Major, D.T, Gao, J., Heroux, A., Orville, A.M., Valley, M.P., Fitzpatrick, P.F. Description: Nitroalkane oxidase: mutant40... |
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The | ==Nitroalkane oxidase: mutant402N crystallized with nitroethane== | ||
<StructureSection load='3fcj' size='340' side='right'caption='[[3fcj]], [[Resolution|resolution]] 2.40Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3fcj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FCJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FCJ 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]] 2.4Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NIE:NITROETHANE'>NIE</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=3fcj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fcj OCA], [https://pdbe.org/3fcj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fcj RCSB], [https://www.ebi.ac.uk/pdbsum/3fcj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fcj ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/NAO_FUSOX NAO_FUSOX] Catalyzes the oxidative denitrification of neutral nitroalkanes, including 3-nitro-2-pentanol, 1-nitropropane, 2-nitropropane, nitroethane and nitrocyclohexane, and may thereby protect the organism against toxic compounds. Has no detectable acyl-CoA dehydrogenase activity.<ref>PMID:11867731</ref> <ref>PMID:22538</ref> <ref>PMID:16430210</ref> | |||
== 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/fc/3fcj_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=3fcj ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution. | |||
Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.,Major DT, Heroux A, Orville AM, Valley MP, Fitzpatrick PF, Gao J Proc Natl Acad Sci U S A. 2009 Nov 19. PMID:19926855<ref>PMID:19926855</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3fcj" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Fusarium oxysporum]] | |||
[[Category: Large Structures]] | |||
[[Category: Fitzpatrick PF]] | |||
[[Category: Gao J]] | |||
[[Category: Heroux A]] | |||
[[Category: Major DT]] | |||
[[Category: Orville AM]] | |||
[[Category: Valley MP]] | |||
Latest revision as of 03:30, 28 December 2023
Nitroalkane oxidase: mutant402N crystallized with nitroethaneNitroalkane oxidase: mutant402N crystallized with nitroethane
Structural highlights
FunctionNAO_FUSOX Catalyzes the oxidative denitrification of neutral nitroalkanes, including 3-nitro-2-pentanol, 1-nitropropane, 2-nitropropane, nitroethane and nitrocyclohexane, and may thereby protect the organism against toxic compounds. Has no detectable acyl-CoA dehydrogenase activity.[1] [2] [3] Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe proton transfer reaction between the substrate nitroethane and Asp-402 catalyzed by nitroalkane oxidase and the uncatalyzed process in water have been investigated using a path-integral free-energy perturbation method. Although the dominating effect in rate acceleration by the enzyme is the lowering of the quasiclassical free energy barrier, nuclear quantum effects also contribute to catalysis in nitroalkane oxidase. In particular, the overall nuclear quantum effects have greater contributions to lowering the classical barrier in the enzyme, and there is a larger difference in quantum effects between proton and deuteron transfer for the enzymatic reaction than that in water. Both experiment and computation show that primary KIEs are enhanced in the enzyme, and the computed Swain-Schaad exponent for the enzymatic reaction is exacerbated relative to that in the absence of the enzyme. In addition, the computed tunneling transmission coefficient is approximately three times greater for the enzyme reaction than the uncatalyzed reaction, and the origin of the difference may be attributed to a narrowing effect in the effective potentials for tunneling in the enzyme than that in aqueous solution. Differential quantum tunneling contributions in nitroalkane oxidase catalyzed and the uncatalyzed proton transfer reaction.,Major DT, Heroux A, Orville AM, Valley MP, Fitzpatrick PF, Gao J Proc Natl Acad Sci U S A. 2009 Nov 19. PMID:19926855[4] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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