3d2d: Difference between revisions

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-{{Seed}}
-[[Image:3d2d.jpg|left|200px]]
-<!--
+==Structure of berberine bridge enzyme in complex with (S)-reticuline==
-The line below this paragraph, containing "STRUCTURE_3d2d", creates the "Structure Box" on the page.
+<StructureSection load='3d2d' size='340' side='right'caption='[[3d2d]], [[Resolution|resolution]] 2.80&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'>[[3d2d]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Eschscholzia_californica Eschscholzia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3D2D 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]] 2.796&#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=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=REN:(S)-RETICULINE'>REN</scene></td></tr>
-{{STRUCTURE_3d2d|  PDB=3d2d  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3d2d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d2d OCA], [https://pdbe.org/3d2d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3d2d RCSB], [https://www.ebi.ac.uk/pdbsum/3d2d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3d2d ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RETO_ESCCA RETO_ESCCA] Essential to the formation of benzophenanthridine alkaloids in the response of plants to pathogenic attack. Catalyzes the stereospecific conversion of the N-methyl moiety of (S)-reticuline into the berberine bridge carbon of (S)-scoulerine.
+== 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/d2/3d2d_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=3d2d ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Berberine bridge enzyme catalyzes the conversion of (S)-reticuline to (S)-scoulerine by formation of a carbon-carbon bond between the N-methyl group and the phenolic ring. We elucidated the structure of berberine bridge enzyme from Eschscholzia californica and determined the kinetic rates for three active site protein variants. Here we propose a catalytic mechanism combining base-catalyzed proton abstraction with concerted carbon-carbon coupling accompanied by hydride transfer from the N-methyl group to the N5 atom of the FAD cofactor.
-===Structure of berberine bridge enzyme in complex with (S)-reticuline===
+A concerted mechanism for berberine bridge enzyme.,Winkler A, Lyskowski A, Riedl S, Puhl M, Kutchan TM, Macheroux P, Gruber K Nat Chem Biol. 2008 Dec;4(12):739-41. Epub 2008 Oct 26. PMID:18953357<ref>PMID:18953357</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3d2d" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-D2D is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Eschscholzia_californica Eschscholzia californica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D2D OCA].
+*[[Reticuline oxidase|Reticuline oxidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Eschscholzia californica]]
-[[Category: Reticuline oxidase]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Gruber K]]
-[[Category: Gruber, K.]]
+[[Category: Lyskowski A]]
-[[Category: Lyskowski, A.]]
+[[Category: Macheroux P]]
-[[Category: Macheroux, P.]]
+[[Category: Winkler A]]
-[[Category: Winkler, A.]]
-[[Category: Alakloid biosynthesis]]
-[[Category: Bi-covalent flavinylation]]
-[[Category: N-glycosylation]]
-[[Category: Oxidoreductase]]
-[[Category: Substrate complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 29 10:57:18 2008''