2zaf

From Proteopedia

(Difference between revisions)

Current revision

Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase

Structural highlights

2zaf is a 4 chain structure with sequence from Fusarium oxysporum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[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 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.,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^[4]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Daubner SC, Gadda G, Valley MP, Fitzpatrick PF. Cloning of nitroalkane oxidase from Fusarium oxysporum identifies a new member of the acyl-CoA dehydrogenase superfamily. Proc Natl Acad Sci U S A. 2002 Mar 5;99(5):2702-7. Epub 2002 Feb 26. PMID:11867731 doi:http://dx.doi.org/10.1073/pnas.052527799
↑ Kido T, Hashizume K, Soda K. Purification and properties of nitroalkane oxidase from Fusarium oxysporum. J Bacteriol. 1978 Jan;133(1):53-8. PMID:22538
↑ Nagpal A, Valley MP, Fitzpatrick PF, Orville AM. Crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover. Biochemistry. 2006 Jan 31;45(4):1138-50. PMID:16430210 doi:10.1021/bi051966w
↑ Fitzpatrick PF, Bozinovski DM, Heroux A, Shaw PG, Valley MP, Orville AM. Mechanistic and structural analyses of the roles of Arg409 and Asp402 in the reaction of the flavoprotein nitroalkane oxidase. Biochemistry. 2007 Dec 4;46(48):13800-8. Epub 2007 Nov 10. PMID:17994768 doi:10.1021/bi701557k

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2zaf"

@@ Line 1: / Line 1: @@
 ==Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase==
-<StructureSection load='2zaf' size='340' side='right' caption='[[2zaf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='2zaf' size='340' side='right'caption='[[2zaf]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2zaf]] is a 4 chain structure with 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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZAF FirstGlance]. <br>
+<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>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene><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]] 2.5&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2reh|2reh]], [[2c0u|2c0u]], [[2c12|2c12]]</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>
-<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitroalkane_oxidase Nitroalkane oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.3.1 1.7.3.1] </span></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=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>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2zaf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zaf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2zaf RCSB], [http://www.ebi.ac.uk/pdbsum/2zaf PDBsum]</span></td></tr>
+</table>
-<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>
+    <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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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;">
@@ Line 26: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2zaf" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 31: / Line 34: @@
 </StructureSection>
 [[Category: Fusarium oxysporum]]
-[[Category: Nitroalkane oxidase]]
+[[Category: Large Structures]]
-[[Category: Bozinovski, D M.]]
+[[Category: Bozinovski DM]]
-[[Category: Fitzpatrick, P F.]]
+[[Category: Fitzpatrick PF]]
-[[Category: Heroux, A.]]
+[[Category: Heroux A]]
-[[Category: Orville, A M.]]
+[[Category: Orville AM]]
-[[Category: Shaw, P G.]]
+[[Category: Shaw PG]]
-[[Category: Valley, M P.]]
+[[Category: Valley MP]]
-[[Category: Flavoenzyme]]
-[[Category: Flavoprotein]]
-[[Category: Nitroalkane]]
-[[Category: Oxidoreductase]]

2zaf

From Proteopedia

Current revision

Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox