2vqb: Difference between revisions

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-[[Image:2vqb.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2vqb", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2vqb|  PDB=2vqb  |  SCENE=  }}
-'''BACTERIAL FLAVIN-CONTAINING MONOOXYGENASE IN COMPLEX WITH NADP: SOAKING IN AERATED SOLUTION'''
+==Bacterial flavin-containing monooxygenase in complex with NADP: soaking in aerated solution==
+<StructureSection load='2vqb' size='340' side='right'caption='[[2vqb]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2vqb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Methylophaga_aminisulfidivorans Methylophaga aminisulfidivorans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VQB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VQB FirstGlance]. <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]] 2.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></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=2vqb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vqb OCA], [https://pdbe.org/2vqb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vqb RCSB], [https://www.ebi.ac.uk/pdbsum/2vqb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vqb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q83XK4_9GAMM Q83XK4_9GAMM]
+== 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/vq/2vqb_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/main_output.php?pdb_ID=2vqb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Flavin-containing monooxygenases (FMOs) are, after cytochromes P450, the most important monooxygenase system in humans and are involved in xenobiotics metabolism and variability in drug response. The x-ray structure of a soluble prokaryotic FMO from Methylophaga sp. strain SK1 has been solved at 2.6-A resolution and is now the protein of known structure with the highest sequence similarity to human FMOs. The structure possesses a two-domain architecture, with both FAD and NADP(+) well defined by the electron density maps. Biochemical analysis shows that the prokaryotic enzyme shares many functional properties with mammalian FMOs, including substrate specificity and the ability to stabilize the hydroperoxyflavin intermediate that is crucial in substrate oxygenation. On the basis of their location in the structure, the nicotinamide ring and the adjacent ribose of NADP(+) turn out to be an integral part of the catalytic site being actively engaged in the stabilization of the oxygenating intermediate. This feature suggests that NADP(H) has a moonlighting role, in that it adopts two binding modes that allow it to function in both flavin reduction and oxygen reactivity modulation, respectively. We hypothesize that a relative domain rotation is needed to bring NADP(H) to these distinct positions inside the active site. Localization of mutations in human FMO3 that are known to cause trimethylaminuria (fish-odor syndrome) in the elucidated FMO structure provides a structural explanation for their biological effects.
-==Overview==
+Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase.,Alfieri A, Malito E, Orru R, Fraaije MW, Mattevi A Proc Natl Acad Sci U S A. 2008 May 6;105(18):6572-7. Epub 2008 Apr 28. PMID:18443301<ref>PMID:18443301</ref>
-Flavin-containing monooxygenases (FMOs) are, after cytochromes P450, the most important monooxygenase system in humans and are involved in xenobiotics metabolism and variability in drug response. The x-ray structure of a soluble prokaryotic FMO from Methylophaga sp. strain SK1 has been solved at 2.6-A resolution and is now the protein of known structure with the highest sequence similarity to human FMOs. The structure possesses a two-domain architecture, with both FAD and NADP(+) well defined by the electron density maps. Biochemical analysis shows that the prokaryotic enzyme shares many functional properties with mammalian FMOs, including substrate specificity and the ability to stabilize the hydroperoxyflavin intermediate that is crucial in substrate oxygenation. On the basis of their location in the structure, the nicotinamide ring and the adjacent ribose of NADP(+) turn out to be an integral part of the catalytic site being actively engaged in the stabilization of the oxygenating intermediate. This feature suggests that NADP(H) has a moonlighting role, in that it adopts two binding modes that allow it to function in both flavin reduction and oxygen reactivity modulation, respectively. We hypothesize that a relative domain rotation is needed to bring NADP(H) to these distinct positions inside the active site. Localization of mutations in human FMO3 that are known to cause trimethylaminuria (fish-odor syndrome) in the elucidated FMO structure provides a structural explanation for their biological effects.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-VQB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Methylophaga_sp._sk1 Methylophaga sp. sk1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VQB OCA].
+</div>
+<div class="pdbe-citations 2vqb" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase., Alfieri A, Malito E, Orru R, Fraaije MW, Mattevi A, Proc Natl Acad Sci U S A. 2008 May 6;105(18):6572-7. Epub 2008 Apr 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18443301 18443301]
+*[[Monooxygenase 3D structures|Monooxygenase 3D structures]]
-[[Category: Methylophaga sp. sk1]]
+== References ==
-[[Category: Single protein]]
+<references/>
-[[Category: Alfieri, A.]]
+__TOC__
-[[Category: Fraaije, M W.]]
+</StructureSection>
-[[Category: Malito, E.]]
+[[Category: Large Structures]]
-[[Category: Mattevi, A.]]
+[[Category: Methylophaga aminisulfidivorans]]
-[[Category: Orru, R.]]
+[[Category: Alfieri A]]
-[[Category: Drug metabolism]]
+[[Category: Fraaije MW]]
-[[Category: Flavin]]
+[[Category: Malito E]]
-[[Category: Nadp]]
+[[Category: Mattevi A]]
-[[Category: Oxidoreductase]]
+[[Category: Orru R]]
-[[Category: Oxygen]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 14 11:40:23 2008''