4q4k

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Revision as of 07:43, 8 February 2023

Crystal structure of nitronate monooxygenase from Pseudomonas aeruginosa PAO1

Structural highlights

4q4k is a 2 chain structure with sequence from Pseudomonas aeruginosa PAO1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NMO_PSEAE Nitronate monooxygenase that uses molecular oxygen to catalyze the oxidative denitrification of alkyl nitronates. The toxin propionate 3-nitronate (P3N) is the best substrate (and the presumed physiological substrate), but this enzyme is also active on other primary and secondary nitronates such as propyl-1-nitronate, ethylnitronate, pentyl-1-nitronate, butyl-1-nitronate and propyl-2-nitronate (PubMed:25002579). Is likely involved in the degradation of P3N, that allows P.aeruginosa PAO1 to grow on 3-nitropropionate/P3N as the sole nitrogen source (PubMed:20382807). Also functions in the detoxification of P3N, a metabolic poison produced by plants and fungi as a defense mechanism (PubMed:25384477). Cannot oxidize nitroalkanes such as 3-nitropropionate, nitroethane, 1-nitropropane, 1-nitrobutane, 1-nitropentane, or 2-nitropropane (PubMed:25002579).^[1] ^[2] ^[3]

Publication Abstract from PubMed

Nitronate monooxygenase (NMO) oxidizes the mitochondrial toxin propionate 3-nitronate (P3N) to malonate semialdehyde. The enzyme has been previously characterized biochemically in fungi, but no structural information is available. Based on amino acid similarity 4,985 genes are annotated in the Gen-Bank as NMO. Of these, 4,424 (i.e., 89%) are bacterial genes, including several Pseudomonads that have been shown to use P3N as growth substrate. Here, we have cloned and expressed the gene PA4202 of Pseudomonas aeruginosa PAO1, purified the resulting protein and characterized it. The enzyme is active on P3N and other alkyl nitronates, but cannot oxidize nitroalkanes. P3N is the best substrate at pH 7.5 and atmospheric oxygen with app(kcat/Km) of 12x106 M-1s-1, appkcat of 1300 s-1 and appKm of 110 muM. Anaerobic reduction of the enzyme with P3N yields a flavosemiquinone, which is formed within 7.5 ms, consistent with this species being a catalytic intermediate. Absorption spectroscopy, mass spectrometry and X-ray crystallography demonstrate a tightly, non-covalently bound FMN in the active site of the enzyme. Thus, PA4202 is the first NMO identified and characterized in bacteria. The X-ray crystal structure of the enzyme was solved at 1.43 A, showing a TIM barrel fold. Four motifs in common with the biochemically characterized NMO from Cyberlindnera saturnus are identified in the structure of bacterial NMO, defining Class I NMO, which includes bacterial, fungal and two animal NMOs. Notably, the only other NMO from Neurospora crassa for which biochemical evidence is available lacks the four motifs, defining Class II NMO.

The Combined Structural and Kinetic Characterization of a Bacterial Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes NMO Class I and II.,Salvi F, Agniswamy J, Yuan H, Vercammen K, Pelicaen R, Cornelis P, Spain J, Weber IT, Gadda G J Biol Chem. 2014 Jul 7. pii: jbc.M114.577791. PMID:25002579^[4]

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

References

↑ Nishino SF, Shin KA, Payne RB, Spain JC. Growth of bacteria on 3-nitropropionic acid as a sole source of carbon, nitrogen, and energy. Appl Environ Microbiol. 2010 Jun;76(11):3590-8. PMID:20382807 doi:10.1128/AEM.00267-10
↑ Salvi F, Agniswamy J, Yuan H, Vercammen K, Pelicaen R, Cornelis P, Spain J, Weber IT, Gadda G. The Combined Structural and Kinetic Characterization of a Bacterial Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes NMO Class I and II. J Biol Chem. 2014 Jul 7. pii: jbc.M114.577791. PMID:25002579 doi:http://dx.doi.org/10.1074/jbc.M114.577791
↑ Vercammen K, Wei Q, Charlier D, Dötsch A, Haüssler S, Schulz S, Salvi F, Gadda G, Spain J, Rybtke ML, Tolker-Nielsen T, Dingemans J, Ye L, Cornelis P. Pseudomonas aeruginosa LysR PA4203 regulator NmoR acts as a repressor of the PA4202 nmoA gene, encoding a nitronate monooxygenase. J Bacteriol. 2015 Mar;197(6):1026-39. PMID:25384477 doi:10.1128/JB.01991-14
↑ Salvi F, Agniswamy J, Yuan H, Vercammen K, Pelicaen R, Cornelis P, Spain J, Weber IT, Gadda G. The Combined Structural and Kinetic Characterization of a Bacterial Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes NMO Class I and II. J Biol Chem. 2014 Jul 7. pii: jbc.M114.577791. PMID:25002579 doi:http://dx.doi.org/10.1074/jbc.M114.577791

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4q4k"

@@ Line 3: / Line 3: @@
 <StructureSection load='4q4k' size='340' side='right'caption='[[4q4k]], [[Resolution|resolution]] 1.44&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4q4k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q4K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Q4K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4q4k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Q4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Q4K FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PA4202 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</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=4q4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q4k OCA], [https://pdbe.org/4q4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4q4k RCSB], [https://www.ebi.ac.uk/pdbsum/4q4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4q4k ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitronate_monooxygenase Nitronate monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.16 1.13.12.16] </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=4q4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4q4k OCA], [http://pdbe.org/4q4k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4q4k RCSB], [http://www.ebi.ac.uk/pdbsum/4q4k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4q4k ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/NMO_PSEAE NMO_PSEAE] Nitronate monooxygenase that uses molecular oxygen to catalyze the oxidative denitrification of alkyl nitronates. The toxin propionate 3-nitronate (P3N) is the best substrate (and the presumed physiological substrate), but this enzyme is also active on other primary and secondary nitronates such as propyl-1-nitronate, ethylnitronate, pentyl-1-nitronate, butyl-1-nitronate and propyl-2-nitronate (PubMed:25002579). Is likely involved in the degradation of P3N, that allows P.aeruginosa PAO1 to grow on 3-nitropropionate/P3N as the sole nitrogen source (PubMed:20382807). Also functions in the detoxification of P3N, a metabolic poison produced by plants and fungi as a defense mechanism (PubMed:25384477). Cannot oxidize nitroalkanes such as 3-nitropropionate, nitroethane, 1-nitropropane, 1-nitrobutane, 1-nitropentane, or 2-nitropropane (PubMed:25002579).<ref>PMID:20382807</ref> <ref>PMID:25002579</ref> <ref>PMID:25384477</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 20: @@
 ==See Also==
-*[[Monooxygenase|Monooxygenase]]
+*[[Monooxygenase 3D structures|Monooxygenase 3D structures]]
 == References ==
 <references/>
@@ Line 26: / Line 26: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Nitronate monooxygenase]]
+[[Category: Pseudomonas aeruginosa PAO1]]
-[[Category: Pseae]]
+[[Category: Agniswamy J]]
-[[Category: Agniswamy, J]]
+[[Category: Gadda G]]
-[[Category: Gadda, G]]
+[[Category: Salvi F]]
-[[Category: Salvi, F]]
+[[Category: Weber IT]]
-[[Category: Weber, I T]]
-[[Category: Fmn binding]]
-[[Category: Oxidoreductase]]
-[[Category: Tim barrel]]

4q4k

From Proteopedia

Revision as of 07:43, 8 February 2023

Crystal structure of nitronate monooxygenase from Pseudomonas aeruginosa PAO1

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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