2d1w: Difference between revisions

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-[[Image:2d1w.png|left|200px]]
-<!--
+==Substrate Schiff-Base intermediate with tyramine in copper amine oxidase from Arthrobacter globiformis==
-The line below this paragraph, containing "STRUCTURE_2d1w", creates the "Structure Box" on the page.
+<StructureSection load='2d1w' size='340' side='right'caption='[[2d1w]], [[Resolution|resolution]] 1.74&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'>[[2d1w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D1W 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]] 1.74&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=TTS:3-((3E)-4-HYDROXY-3-{[2-(4-HYDROXYPHENYL)ETHYL]IMINO}-6-OXOCYCLOHEXA-1,4-DIEN-1-YL)ALANINE'>TTS</scene></td></tr>
-{{STRUCTURE_2d1w|  PDB=2d1w  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d1w OCA], [https://pdbe.org/2d1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d1w RCSB], [https://www.ebi.ac.uk/pdbsum/2d1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d1w ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PAOX_ARTGO PAOX_ARTGO]
+== 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/d1/2d1w_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2d1w ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A key step decisively affecting the catalytic efficiency of copper amine oxidase is stereospecific abstraction of substrate alpha-proton by a conserved Asp residue. We analyzed this step by pre-steady-state kinetics using a bacterial enzyme and stereospecifically deuterium-labeled substrates, 2-phenylethylamine and tyramine. A small and temperature-dependent kinetic isotope effect (KIE) was observed with 2-phenylethylamine, whereas a large and temperature-independent KIE was observed with tyramine in the alpha-proton abstraction step, showing that this step is driven by quantum mechanical hydrogen tunneling rather than the classical transition-state mechanism. Furthermore, an Arrhenius-type preexponential factor ratio approaching a transition-state value was obtained in the reaction of a mutant enzyme lacking the critical Asp. These results provide strong evidence for enzyme-enhanced hydrogen tunneling. X-ray crystallographic structures of the reaction intermediates revealed a small difference in the binding mode of distal parts of substrates, which would modulate hydrogen tunneling proceeding through either active or passive dynamics.
-===Substrate Schiff-Base intermediate with tyramine in copper amine oxidase from Arthrobacter globiformis===
+Quantum mechanical hydrogen tunneling in bacterial copper amine oxidase reaction.,Murakawa T, Okajima T, Kuroda S, Nakamoto T, Taki M, Yamamoto Y, Hayashi H, Tanizawa K Biochem Biophys Res Commun. 2006 Apr 7;342(2):414-23. Epub 2006 Feb 8. PMID:16487484<ref>PMID:16487484</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_16487484}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2d1w" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16487484 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_16487484}}
-==About this Structure==
-[[2d1w]] is a 2 chain structure of [[Copper Amine Oxidase]] with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D1W OCA].
 ==See Also==
 *[[Copper Amine Oxidase|Copper Amine Oxidase]]
+*[[Copper amine oxidase 3D structures|Copper amine oxidase 3D structures]]
-==Reference==
+== References ==
-<ref group="xtra">PMID:016487484</ref><references group="xtra"/>
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arthrobacter globiformis]]
-[[Category: Oxidoreductase]]
+[[Category: Large Structures]]
-[[Category: Hayashi, H.]]
+[[Category: Hayashi H]]
-[[Category: Kuroda, S.]]
+[[Category: Kuroda S]]
-[[Category: Murakawa, T.]]
+[[Category: Murakawa T]]
-[[Category: Nakamoto, T.]]
+[[Category: Nakamoto T]]
-[[Category: Okajima, T.]]
+[[Category: Okajima T]]
-[[Category: Taki, M.]]
+[[Category: Taki M]]
-[[Category: Tanizawa, K.]]
+[[Category: Tanizawa K]]
-[[Category: Yamamoto, Y.]]
+[[Category: Yamamoto Y]]
-[[Category: Amine oxidase]]
-[[Category: Oxidoreductase]]
-[[Category: Reaction intermediate]]
-[[Category: Substrate schiff-base]]
-[[Category: Topaquinone]]
-[[Category: Tpq]]