2zaf: Difference between revisions

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-{{Seed}}
-[[Image:2zaf.png|left|200px]]
-<!--
+==Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase==
-The line below this paragraph, containing "STRUCTURE_2zaf", creates the "Structure Box" on the page.
+<StructureSection load='2zaf' size='340' side='right'caption='[[2zaf]], [[Resolution|resolution]] 2.50&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'>[[2zaf]] 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=2ZAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZAF 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]] 2.5&#8491;</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></td></tr>
-{{STRUCTURE_2zaf|  PDB=2zaf  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2zaf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zaf OCA], [https://pdbe.org/2zaf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zaf RCSB], [https://www.ebi.ac.uk/pdbsum/2zaf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zaf 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/za/2zaf_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=2zaf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The flavoprotein nitroalkane oxidase (NAO) catalyzes the oxidation of primary and secondary nitroalkanes to the corresponding aldehydes and ketones. The enzyme is a homologue of acyl-CoA dehydrogenase. Asp402 in NAO has been proposed to be the active site base responsible for removing the substrate proton in the first catalytic step; structurally it corresponds to the glutamate which acts as the base in medium chain acyl-CoA dehydrogenase. In the active site of NAO, the carboxylate of Asp402 forms an ionic interaction with the side chain of Arg409. The R409K enzyme has now been characterized kinetically and structurally. The mutation results in a decrease in the rate constant for proton abstraction of 100-fold. Analysis of the three-dimensional structure of the R409K enzyme, determined by X-ray crystallography to a resolution of 2.65 A, shows that the critical structural change is an increase in the distance between the carboxylate of Asp402 and the positively charged nitrogen in the side chain of the residue at position 409. The D402E mutation results in a smaller decrease in the rate constant for proton abstraction of 18-fold. The structure of the D402E enzyme, determined at 2.4 A resolution, shows that there is a smaller increase in the distance between Arg409 and the carboxylate at position 402, and the interaction of this residue with Ser276 is perturbed. These results establish the critical importance of the interaction between Asp402 and Arg409 for proton abstraction by nitroalkane oxidase.
-===Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase===
+Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase.,Fitzpatrick PF, Bozinovski DM, Heroux A, Shaw PG, Valley MP, Orville AM Biochemistry. 2007 Dec 4;46(48):13800-8. Epub 2007 Nov 10. PMID:17994768<ref>PMID:17994768</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_17994768}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2zaf" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17994768 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17994768}}
+__TOC__
+</StructureSection>
-==About this Structure==
-ZAF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Fusarium_oxysporum Fusarium oxysporum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZAF OCA].
-==Reference==
-Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase., Fitzpatrick PF, Bozinovski DM, Heroux A, Shaw PG, Valley MP, Orville AM, Biochemistry. 2007 Dec 4;46(48):13800-8. Epub 2007 Nov 10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17994768 17994768]
-Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover., Nagpal A, Valley MP, Fitzpatrick PF, Orville AM, Biochemistry. 2006 Jan 31;45(4):1138-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16430210 16430210]
 [[Category: Fusarium oxysporum]]
-[[Category: Nitroalkane oxidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Bozinovski DM]]
-[[Category: Bozinovski, D M.]]
+[[Category: Fitzpatrick PF]]
-[[Category: Fitzpatrick, P F.]]
+[[Category: Heroux A]]
-[[Category: Heroux, A.]]
+[[Category: Orville AM]]
-[[Category: Orville, A M.]]
+[[Category: Shaw PG]]
-[[Category: Shaw, P G.]]
+[[Category: Valley MP]]
-[[Category: Valley, M P.]]
-[[Category: Flavoenzyme]]
-[[Category: Flavoprotein]]
-[[Category: Nitroalkane]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 14:37:01 2008''