3ng7

From Proteopedia

(Difference between revisions)

Current revision

Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity

Structural highlights

3ng7 is a 1 chain structure with sequence from Paenarthrobacter nicotinovorans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HLNO_PAENI Involved in the degradation of L-nicotine (PubMed:5849820). Catalyzes the oxidation of (S)-6-hydroxynicotine (6-hydroxy-L-nicotine) to 6-hydroxypseudooxynicotine (PubMed:5849820, PubMed:4965794, PubMed:5646150, PubMed:21383134, PubMed:26744768, PubMed:28080034). Oxidation of the pyrrolidine ring of (S)-6-hydroxynicotine leads to the formation of the optically inactive 6-hydroxy-N-methylmyosmine, which hydrolyzes spontaneously to 6-hydroxypseudooxynicotine (PubMed:4965794, PubMed:21383134, PubMed:26744768, PubMed:28080034). Acts with absolute stereospecificity on the L-form of 6-hydroxynicotine (PubMed:4965794). Can also use (S)-6-hydroxynornicotine (PubMed:26744768, PubMed:28080034).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Publication Abstract from PubMed

FAD-linked oxidases constitute a class of enzymes which catalyze dehydrogenation as a fundamental biochemical reaction, followed by reoxidation of reduced flavin. Here, we present high-resolution crystal structures showing the flavoenzyme 6-hydroxy-l-nicotine oxidase in action. This enzyme was trapped during catalytic degradation of the native substrate in a sequence of discrete reaction states corresponding to the substrate-reduced enzyme, a complex of the enzyme with the intermediate enamine product and formation of the final aminoketone product. The inactive d-stereoisomer binds in mirror symmetry with respect to the catalytic axis, revealing absolute stereospecificity of hydrogen transfer to the flavin. The structural data suggest deprotonation of the substrate when bound at the active site, an overall binary complex mechanism and oxidation by direct hydride transfer. The amine nitrogen has a critical role in the dehydrogenation step and may activate carbocation formation at the alpha-carbon via delocalization from the lone pair to sigma* C(alpha)-H. Enzymatically assisted hydrolysis of the intermediate product occurs at a remote (P site) cavity. Substrate entry and product exit follow different paths. Structural and kinetic data suggest that substrate can also bind to the reduced enzyme, associated with slower reoxidation as compared to the rate of reoxidation of free enzyme. The results are of general relevance for the mechanisms of flavin amine oxidases.

Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family.,Kachalova G, Decker K, Holt A, Bartunik HD Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4800-5. Epub 2011 Mar 7. PMID:21383134^[7]

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

References

↑ Kachalova G, Decker K, Holt A, Bartunik HD. Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4800-5. Epub 2011 Mar 7. PMID:21383134 doi:http://dx.doi.org/10.1073/pnas.1016684108
↑ Fitzpatrick PF, Chadegani F, Zhang S, Roberts KM, Hinck CS. Mechanism of the Flavoprotein L-Hydroxynicotine Oxidase: Kinetic Mechanism, Substrate Specificity, Reaction Product, and Roles of Active-Site Residues. Biochemistry. 2016 Feb 2;55(4):697-703. PMID:26744768 doi:10.1021/acs.biochem.5b01325
↑ Fitzpatrick PF, Chadegani F, Zhang S, Dougherty V. Mechanism of Flavoprotein l-6-Hydroxynicotine Oxidase: pH and Solvent Isotope Effects and Identification of Key Active Site Residues. Biochemistry. 2017 Feb 14;56(6):869-875. PMID:28080034 doi:10.1021/acs.biochem.6b01160
↑ Decker K, Dai VD. Mechanism and specifcity of L Eur J Biochem. 1967 Dec;3(2):132-8. PMID:4965794 doi:10.1111/j.1432-1033.1967.tb19507.x
↑ Dai VD, Decker K, Sund H. Purification and properties of L-6-hydroxynicotine oxidase. Eur J Biochem. 1968 Mar;4(1):95-102. PMID:5646150 doi:10.1111/j.1432-1033.1968.tb00177.x
↑ Decker K, Bleeg H. Induction and purification of stereospecific nicotine oxidizing enzymes from Arthrobacter oxidans. Biochim Biophys Acta. 1965 Aug 24;105(2):313-24. PMID:5849820 doi:10.1016/s0926-6593(65)80155-2
↑ Kachalova G, Decker K, Holt A, Bartunik HD. Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family. Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4800-5. Epub 2011 Mar 7. PMID:21383134 doi:http://dx.doi.org/10.1073/pnas.1016684108

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3ng7"

Categories: Large Structures | Paenarthrobacter nicotinovorans | Bartunik HD | Kachalova GS

@@ Line 1: / Line 1: @@
-[[Image:3ng7.jpg|left|200px]]
-<!--
+==Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity==
-The line below this paragraph, containing "STRUCTURE_3ng7", creates the "Structure Box" on the page.
+<StructureSection load='3ng7' size='340' side='right'caption='[[3ng7]], [[Resolution|resolution]] 1.95&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'>[[3ng7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenarthrobacter_nicotinovorans Paenarthrobacter nicotinovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NG7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NG7 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]] 1.95&#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>, <scene name='pdbligand=GP7:(1R)-2-{[(S)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(PENTADECANOYLOXY)METHYL]ETHYL+(12E)-HEXADECA-9,12-DIENOATE'>GP7</scene>, <scene name='pdbligand=HNK:5-[(2R)-1-METHYLPYRROLIDIN-2-YL]PYRIDIN-2-OL'>HNK</scene>, <scene name='pdbligand=HNL:5-[(2S)-1-METHYLPYRROLIDIN-2-YL]PYRIDIN-2-OL'>HNL</scene></td></tr>
-{{STRUCTURE_3ng7|  PDB=3ng7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ng7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ng7 OCA], [https://pdbe.org/3ng7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ng7 RCSB], [https://www.ebi.ac.uk/pdbsum/3ng7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ng7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HLNO_PAENI HLNO_PAENI] Involved in the degradation of L-nicotine (PubMed:5849820). Catalyzes the oxidation of (S)-6-hydroxynicotine (6-hydroxy-L-nicotine) to 6-hydroxypseudooxynicotine (PubMed:5849820, PubMed:4965794, PubMed:5646150, PubMed:21383134, PubMed:26744768, PubMed:28080034). Oxidation of the pyrrolidine ring of (S)-6-hydroxynicotine leads to the formation of the optically inactive 6-hydroxy-N-methylmyosmine, which hydrolyzes spontaneously to 6-hydroxypseudooxynicotine (PubMed:4965794, PubMed:21383134, PubMed:26744768, PubMed:28080034). Acts with absolute stereospecificity on the L-form of 6-hydroxynicotine (PubMed:4965794). Can also use (S)-6-hydroxynornicotine (PubMed:26744768, PubMed:28080034).<ref>PMID:21383134</ref> <ref>PMID:26744768</ref> <ref>PMID:28080034</ref> <ref>PMID:4965794</ref> <ref>PMID:5646150</ref> <ref>PMID:5849820</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+FAD-linked oxidases constitute a class of enzymes which catalyze dehydrogenation as a fundamental biochemical reaction, followed by reoxidation of reduced flavin. Here, we present high-resolution crystal structures showing the flavoenzyme 6-hydroxy-l-nicotine oxidase in action. This enzyme was trapped during catalytic degradation of the native substrate in a sequence of discrete reaction states corresponding to the substrate-reduced enzyme, a complex of the enzyme with the intermediate enamine product and formation of the final aminoketone product. The inactive d-stereoisomer binds in mirror symmetry with respect to the catalytic axis, revealing absolute stereospecificity of hydrogen transfer to the flavin. The structural data suggest deprotonation of the substrate when bound at the active site, an overall binary complex mechanism and oxidation by direct hydride transfer. The amine nitrogen has a critical role in the dehydrogenation step and may activate carbocation formation at the alpha-carbon via delocalization from the lone pair to sigma* C(alpha)-H. Enzymatically assisted hydrolysis of the intermediate product occurs at a remote (P site) cavity. Substrate entry and product exit follow different paths. Structural and kinetic data suggest that substrate can also bind to the reduced enzyme, associated with slower reoxidation as compared to the rate of reoxidation of free enzyme. The results are of general relevance for the mechanisms of flavin amine oxidases.
-===Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity===
+Crystallographic snapshots of the complete reaction cycle of nicotine degradation by an amine oxidase of the monoamine oxidase (MAO) family.,Kachalova G, Decker K, Holt A, Bartunik HD Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4800-5. Epub 2011 Mar 7. PMID:21383134<ref>PMID:21383134</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_20006620}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3ng7" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20006620 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20006620}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-[[3ng7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_nicotinovorans Arthrobacter nicotinovorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NG7 OCA].
+[[Category: Paenarthrobacter nicotinovorans]]
+[[Category: Bartunik HD]]
-==Reference==
+[[Category: Kachalova GS]]
-<ref group="xtra">PMID:20006620</ref><references group="xtra"/>
-[[Category: Arthrobacter nicotinovorans]]
-[[Category: Bartunik, H D.]]
-[[Category: Kachalova, G S.]]

3ng7

From Proteopedia

Current revision

Complex of dithionite-reduced 6-hydroxy-L-nicotine oxidase with substrate bound at active site and inhibitor at exit cavity

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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