This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3d9d

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 04:00, 5 August 2016

Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane

Structural highlights

3d9d is a 4 chain structure with sequence from Fusox. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2c12, 2c0u, 2reh, 2zaf, 3d9e, 3d9f, 3d9g
Activity:	Nitroalkane oxidase, with EC number 1.7.3.1
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 flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 A resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes [Valley, M. P., and Fitzpatrick, P. F. (2003) J. Am. Chem. Soc. 125, 8738-8739]. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped [Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066]. The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction (dagger) (double dagger).,Heroux A, Bozinovski DM, Valley MP, Fitzpatrick PF, Orville AM Biochemistry. 2009 Mar 27. PMID:19265437^[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
↑ Heroux A, Bozinovski DM, Valley MP, Fitzpatrick PF, Orville AM. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction (dagger) (double dagger). Biochemistry. 2009 Mar 27. PMID:19265437 doi:10.1021/bi8023042

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/3d9d"

@@ Line 1: / Line 1: @@
 ==Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane==
 <StructureSection load='3d9d' size='340' side='right' caption='[[3d9d]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c12|2c12]], [[2c0u|2c0u]], [[2reh|2reh]], [[2zaf|2zaf]], [[3d9e|3d9e]], [[3d9f|3d9f]], [[3d9g|3d9g]]</td></tr>
 <tr id='activity'><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3d9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d9d RCSB], [http://www.ebi.ac.uk/pdbsum/3d9d PDBsum]</span></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=3d9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d9d OCA], [http://pdbe.org/3d9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3d9d RCSB], [http://www.ebi.ac.uk/pdbsum/3d9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3d9d ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 18: / Line 19: @@
     <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=3d9d ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 28: / Line 29: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 3d9d" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>

3d9d

From Proteopedia

Revision as of 04:00, 5 August 2016

Nitroalkane oxidase: mutant D402N crystallized with 1-nitrohexane

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