2cwu: Difference between revisions

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-{{Seed}}
-[[Image:2cwu.png|left|200px]]
-<!--
+==Substrate schiff-base intermediate of copper amine oxidase from arthrobacter globiformis==
-The line below this paragraph, containing "STRUCTURE_2cwu", creates the "Structure Box" on the page.
+<StructureSection load='2cwu' size='340' side='right'caption='[[2cwu]], [[Resolution|resolution]] 1.85&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'>[[2cwu]] 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=2CWU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CWU 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]] 1.85&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1TY:3-{(3E)-4-HYDROXY-6-OXO-3-[(2-PHENYLETHYL)IMINO]CYCLOHEXA-1,4-DIEN-1-YL}ALANINE'>1TY</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene></td></tr>
-{{STRUCTURE_2cwu|  PDB=2cwu  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2cwu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cwu OCA], [https://pdbe.org/2cwu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cwu RCSB], [https://www.ebi.ac.uk/pdbsum/2cwu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cwu 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/cw/2cwu_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=2cwu ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Copper amine oxidase contains a post-translationally generated quinone cofactor, topa quinone (TPQ), which mediates electron transfer from the amine substrate to molecular oxygen. The overall catalytic reaction is divided into the former reductive and the latter oxidative half-reactions based on the redox state of TPQ. In the reductive half-reaction, substrate amine reacts with the C5 carbonyl group of the oxidized TPQ, forming the substrate Schiff base (TPQ(ssb)), which is then converted to the product Schiff base (TPQ(psb)). During this step, an invariant Asp residue with an elevated pKa is presumed to serve as a general base accepting the alpha proton of the substrate. When Asp298, the putative active-site base in the recombinant enzyme from Arthrobacter globiformis, was mutated into Ala, the catalytic efficiency dropped to a level of about 10(6) orders of magnitude smaller than the wild-type (WT) enzyme, consistent with the essentiality of Asp298. Global analysis of the slow UV/vis spectral changes observed during the reductive half-reaction of the D298A mutant with 2-phenylethylamine provided apparent rate constants for the formation and decay of TPQ(ssb) (k(obs) = 4.7 and 4.8 x 10(-4) s(-1), respectively), both of which are markedly smaller than those of the WT enzyme determined by rapid-scan stopped-flow analysis (k(obs) = 699 and 411 s(-1), respectively). Thus, Asp298 plays important roles not only in the alpha-proton abstraction from TPQ(ssb) but also in other steps in the reductive half-reaction. X-ray diffraction analyses of D298A crystals soaked with the substrate for 1 h and 1 week revealed the structures of TPQ(ssb) and TPQ(psb), respectively, as pre-assigned by single-crystal microspectrophotometry. Consistent with the stereospecificity of alpha-proton abstraction, the pro-S alpha-proton of TPQ(ssb) to be abstracted is positioned nearly perpendicularly to the plane formed by the Schiff-base imine double bond conjugating with the quinone ring of TPQ, so that the orbitals of sigma and pi electrons maximally overlap in the conjugate system. More intriguingly, the pro-S alpha proton of the substrate is released stereospecifically even in the reaction catalyzed by the base-lacking D298A mutant. On the basis of these results, we propose that the stereospecificity of alpha-proton abstraction is primarily determined by the conformation of TPQ(ssb), rather than the relative geometry of TPQ and the catalytic base.
-===Substrate schiff-base intermediate of copper amine oxidase from arthrobacter globiformis===
+Kinetic and structural studies on the catalytic role of the aspartic acid residue conserved in copper amine oxidase.,Chiu YC, Okajima T, Murakawa T, Uchida M, Taki M, Hirota S, Kim M, Yamaguchi H, Kawano Y, Kamiya N, Kuroda S, Hayashi H, Yamamoto Y, Tanizawa K Biochemistry. 2006 Apr 4;45(13):4105-20. PMID:16566584<ref>PMID:16566584</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2cwu" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16566584}}, adds the Publication Abstract to the page
+*[[Copper amine oxidase 3D structures|Copper amine oxidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16566584 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16566584}}
+__TOC__
+</StructureSection>
-==About this Structure==
-CWU is a 2 chains structure of sequences 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=2CWU OCA].
-==Reference==
-<ref group="xtra">PMID:16566584</ref><references group="xtra"/>
 [[Category: Arthrobacter globiformis]]
-[[Category: Chiu, Y C.]]
+[[Category: Large Structures]]
-[[Category: Hayashi, H.]]
+[[Category: Chiu YC]]
-[[Category: Hirota, S.]]
+[[Category: Hayashi H]]
-[[Category: Kamiya, N.]]
+[[Category: Hirota S]]
-[[Category: Kawano, Y.]]
+[[Category: Kamiya N]]
-[[Category: Kim, M.]]
+[[Category: Kawano Y]]
-[[Category: Kuroda, S.]]
+[[Category: Kim M]]
-[[Category: Murakawa, T.]]
+[[Category: Kuroda S]]
-[[Category: Okajima, T.]]
+[[Category: Murakawa T]]
-[[Category: Taki, M.]]
+[[Category: Okajima T]]
-[[Category: Tanizawa, K.]]
+[[Category: Taki M]]
-[[Category: Uchida, M.]]
+[[Category: Tanizawa K]]
-[[Category: Yamaguchi, H.]]
+[[Category: Uchida M]]
-[[Category: Yamamoto, Y.]]
+[[Category: Yamaguchi H]]
-[[Category: 2-phenethylamine]]
+[[Category: Yamamoto Y]]
-[[Category: Amine oxidase]]
-[[Category: Catalytic base]]
-[[Category: Copper]]
-[[Category: Reaction intermediate]]
-[[Category: Topaquinone]]
-[[Category: Tpq]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:02:30 2009''