2c12

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor

Structural highlights

2c12 is a 6 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 2.07Å
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

Nitroalkane oxidase (NAO) from Fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of H(2)O(2) and nitrite. The flavoenzyme is a new member of the acyl-CoA dehydrogenase (ACAD) family, but it does not react with acyl-CoA substrates. We present the 2.2 A resolution crystal structure of NAO trapped during the turnover of nitroethane as a covalent N5-FAD adduct (ES*). The homotetrameric structure of ES* was solved by MAD phasing with 52 Se-Met sites in an orthorhombic space group. The electron density for the N5-(2-nitrobutyl)-1,5-dihydro-FAD covalent intermediate is clearly resolved. The structure of ES was used to solve the crystal structure of oxidized NAO at 2.07 A resolution. The c axis for the trigonal space group of oxidized NAO is 485 A, and there are six subunits (1(1)/(2) holoenzymes) in the asymmetric unit. Four of the active sites contain spermine (EI), a weak competitive inhibitor, and two do not contain spermine (E(ox)). The active-site structures of E(ox), EI, and ES* reveal a hydrophobic channel that extends from the exterior of the protein and terminates at Asp402 and the N5 position on the re face of the FAD. Thus, Asp402 is in the correct position to serve as the active-site base, where it is proposed to abstract the alpha proton from neutral nitroalkane substrates. The structures for NAO and various members of the ACAD family overlay with root-mean-square deviations between 1.7 and 3.1 A. The homologous region typically spans more than 325 residues and includes Glu376, which is the active-site base in the prototypical member of the ACAD family. However, NAO and the ACADs exhibit differences in hydrogen-bonding patterns between the respective active-site base, substrate molecules, and FAD. These likely differentiate NAO from the homologues and, consequently, are proposed to result in the unique reaction mechanism of NAO.

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:16430210^[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
↑ 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

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/2c12"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor==
-<StructureSection load='2c12' size='340' side='right' caption='[[2c12]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
+<StructureSection load='2c12' size='340' side='right'caption='[[2c12]], [[Resolution|resolution]] 2.07&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c12]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Fusox Fusox]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C12 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c12]] is a 6 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=2C12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C12 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.07&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c0u|2c0u]]</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=PE4:2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL'>PE4</scene>, <scene name='pdbligand=SPM:SPERMINE'>SPM</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2c12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c12 OCA], [http://pdbe.org/2c12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2c12 RCSB], [http://www.ebi.ac.uk/pdbsum/2c12 PDBsum]</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=2c12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c12 OCA], [https://pdbe.org/2c12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c12 RCSB], [https://www.ebi.ac.uk/pdbsum/2c12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c12 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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/c1/2c12_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c1/2c12_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=2c12 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Fusox]]
+[[Category: Fusarium oxysporum]]
-[[Category: Fitzpatrick, P F]]
+[[Category: Large Structures]]
-[[Category: Nagpal, A]]
+[[Category: Fitzpatrick PF]]
-[[Category: Orville, A M]]
+[[Category: Nagpal A]]
-[[Category: Valley, M P]]
+[[Category: Orville AM]]
-[[Category: Acyl-coa dehydrogenase]]
+[[Category: Valley MP]]
-[[Category: Fad]]
-[[Category: Flavoenzyme]]
-[[Category: Flavoprotein]]
-[[Category: Inhibitor]]
-[[Category: Long cell edge]]
-[[Category: Nitroalkane]]
-[[Category: Oxidoreductase]]

2c12

From Proteopedia

Current revision

Crystal Structure of Nitroalkane Oxidase in Complex with Spermine, a Competitive Inhibitor

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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